From 9ad0197c398751b4fddf88e0002537344da94f4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=9Clgen=20Sar=C4=B1kavak?= Date: Fri, 24 Apr 2026 21:12:22 +0300 Subject: [PATCH] Apply UP009 fixes --- anvio/__init__.py | 1 - anvio/agglomeration.py | 1 - anvio/argparse.py | 1 - anvio/artifacts/samples_txt.py | 1 - anvio/authors.py | 1 - anvio/auxiliarydataops.py | 1 - anvio/bamops.py | 1 - anvio/bottleroutes.py | 1 - anvio/cazymes.py | 1 - anvio/ccollections.py | 1 - anvio/cli/add_default_collection.py | 1 - anvio/cli/analyze_synteny.py | 1 - anvio/cli/annotate_fragmented_genes.py | 1 - anvio/cli/as_markdown.py | 1 - anvio/cli/augustus_output_to_external_gene_calls.py | 1 - anvio/cli/checkm_tree_to_interactive.py | 1 - anvio/cli/cluster_contigs.py | 1 - anvio/cli/compute_ani.py | 1 - anvio/cli/compute_ani_for_fasta.py | 1 - anvio/cli/compute_bayesian_pan_core.py | 1 - anvio/cli/compute_completeness.py | 1 - anvio/cli/compute_functional_enrichment.py | 1 - anvio/cli/compute_functional_enrichment_across_genomes.py | 1 - anvio/cli/compute_functional_enrichment_in_pan.py | 1 - anvio/cli/compute_gene_cluster_homogeneity.py | 1 - anvio/cli/compute_genome_similarity.py | 1 - anvio/cli/compute_metabolic_enrichment.py | 1 - anvio/cli/compute_rarefaction_curves.py | 1 - anvio/cli/db_info.py | 1 - anvio/cli/delete_collection.py | 1 - anvio/cli/delete_functions.py | 1 - anvio/cli/delete_hmms.py | 1 - anvio/cli/delete_misc_data.py | 1 - anvio/cli/delete_state.py | 1 - anvio/cli/dereplicate_genomes.py | 1 - anvio/cli/display_codon_frequencies.py | 1 - anvio/cli/display_contigs_stats.py | 1 - anvio/cli/display_functions.py | 1 - anvio/cli/display_metabolism.py | 1 - anvio/cli/display_pan.py | 1 - anvio/cli/display_structure.py | 1 - anvio/cli/draw_kegg_pathways.py | 1 - anvio/cli/estimate_genome_completeness.py | 1 - anvio/cli/estimate_genome_size.py | 1 - anvio/cli/estimate_genome_taxonomy.py | 1 - anvio/cli/estimate_metabolic_independence.py | 1 - anvio/cli/estimate_metabolism.py | 1 - anvio/cli/estimate_scg_taxonomy.py | 1 - anvio/cli/estimate_trna_taxonomy.py | 1 - anvio/cli/experimental_organization.py | 1 - anvio/cli/export_collection.py | 1 - anvio/cli/export_contigs.py | 1 - anvio/cli/export_functions.py | 1 - anvio/cli/export_gene_calls.py | 1 - anvio/cli/export_gene_clusters.py | 1 - anvio/cli/export_gene_coverage_and_detection.py | 1 - anvio/cli/export_items_order.py | 1 - anvio/cli/export_locus.py | 1 - anvio/cli/export_misc_data.py | 1 - anvio/cli/export_splits_and_coverages.py | 1 - anvio/cli/export_splits_taxonomy.py | 1 - anvio/cli/export_state.py | 1 - anvio/cli/export_structures.py | 1 - anvio/cli/export_table.py | 1 - anvio/cli/filter_fasta_by_blast.py | 1 - anvio/cli/filter_hmm_hits_table.py | 1 - anvio/cli/find_misassemblies.py | 1 - anvio/cli/fix_homopolymer_indels.py | 1 - anvio/cli/gen_CPR_classifier.py | 1 - anvio/cli/gen_contigs_database.py | 1 - anvio/cli/gen_defense_finder_models_to_hmm_directory.py | 1 - anvio/cli/gen_distribution_of_genes_in_a_bin.py | 1 - anvio/cli/gen_fixation_index_matrix.py | 1 - anvio/cli/gen_function_matrix_across_genomes.py | 1 - anvio/cli/gen_functions_per_group_stats_output.py | 1 - anvio/cli/gen_gene_consensus_sequences.py | 1 - anvio/cli/gen_gene_level_stats_databases.py | 1 - anvio/cli/gen_genomes_file.py | 1 - anvio/cli/gen_genomes_storage.py | 1 - anvio/cli/gen_help_pages.py | 1 - anvio/cli/gen_hmm_hits_matrix_across_genomes.py | 1 - anvio/cli/gen_network.py | 1 - anvio/cli/gen_phylogenomic_tree.py | 1 - anvio/cli/gen_programs_network.py | 1 - anvio/cli/gen_programs_vignette.py | 1 - anvio/cli/gen_pseudo_paired_reads_from_fastq.py | 1 - anvio/cli/gen_reads.py | 1 - anvio/cli/gen_scg_domain_classifier.py | 1 - anvio/cli/gen_short_reads.py | 1 - anvio/cli/gen_structure_database.py | 1 - anvio/cli/gen_user_module_file.py | 1 - anvio/cli/gen_variability_network.py | 1 - anvio/cli/gen_variability_profile.py | 1 - anvio/cli/get_aa_counts.py | 1 - anvio/cli/get_codon_frequencies.py | 1 - anvio/cli/get_codon_usage_bias.py | 1 - anvio/cli/get_collection_info.py | 1 - anvio/cli/get_coverage_from_bam.py | 1 - anvio/cli/get_hmm_hits_per_gene_call.py | 1 - anvio/cli/get_metabolic_model_file.py | 1 - anvio/cli/get_pn_ps_ratio.py | 1 - anvio/cli/get_sequences_for_gene_calls.py | 1 - anvio/cli/get_sequences_for_gene_clusters.py | 1 - anvio/cli/get_sequences_for_hmm_hits.py | 1 - anvio/cli/get_short_reads_from_bam.py | 1 - anvio/cli/get_short_reads_mapping_to_a_gene.py | 1 - anvio/cli/get_split_coverages.py | 1 - anvio/cli/get_tlen_dist_from_bam.py | 1 - anvio/cli/hmm_to_hmm_directory.py | 1 - anvio/cli/import_collection.py | 1 - anvio/cli/import_functions.py | 1 - anvio/cli/import_items_order.py | 1 - anvio/cli/import_metabolite_profile.py | 1 - anvio/cli/import_misc_data.py | 1 - anvio/cli/import_protein_profile.py | 1 - anvio/cli/import_state.py | 1 - anvio/cli/import_taxonomy_for_genes.py | 1 - anvio/cli/import_taxonomy_for_layers.py | 1 - anvio/cli/init_bam.py | 1 - anvio/cli/inspect.py | 1 - anvio/cli/interactive.py | 1 - anvio/cli/matrix_to_newick.py | 1 - anvio/cli/mcg_classifier.py | 1 - anvio/cli/merge.py | 1 - anvio/cli/merge_bins.py | 1 - anvio/cli/merge_collections.py | 1 - anvio/cli/merge_trnaseq.py | 1 - anvio/cli/meta_pan_genome.py | 1 - anvio/cli/migrate.py | 1 - anvio/cli/oligotype_linkmers.py | 1 - anvio/cli/pan_genome.py | 1 - anvio/cli/permute_trnaseq_seeds.py | 1 - anvio/cli/pfam_accessions_to_hmms_directory.py | 1 - anvio/cli/plot_trnaseq.py | 1 - anvio/cli/predict_CPR_genomes.py | 1 - anvio/cli/predict_metabolic_exchanges.py | 1 - anvio/cli/process_genbank.py | 1 - anvio/cli/process_genbank_metadata.py | 1 - anvio/cli/profile.py | 1 - anvio/cli/profile_blitz.py | 1 - anvio/cli/push.py | 1 - anvio/cli/reaction_network.py | 1 - anvio/cli/refine.py | 1 - anvio/cli/reformat_bam.py | 1 - anvio/cli/reformat_fasta.py | 1 - anvio/cli/rename_bins.py | 1 - anvio/cli/reorient_genomes.py | 1 - anvio/cli/report_circularity.py | 1 - anvio/cli/report_inversions.py | 1 - anvio/cli/report_linkmers.py | 1 - anvio/cli/run_cazymes.py | 1 - anvio/cli/run_eggnog_mapper.py | 1 - anvio/cli/run_hmms.py | 1 - anvio/cli/run_interacdome.py | 1 - anvio/cli/run_kegg_kofams.py | 1 - anvio/cli/run_ncbi_cogs.py | 1 - anvio/cli/run_pfams.py | 1 - anvio/cli/run_scg_taxonomy.py | 1 - anvio/cli/run_trna_taxonomy.py | 1 - anvio/cli/run_workflow.py | 1 - anvio/cli/scan_trnas.py | 1 - anvio/cli/search_functions.py | 1 - anvio/cli/search_palindromes.py | 1 - anvio/cli/search_primers.py | 1 - anvio/cli/search_sequence_motifs.py | 1 - anvio/cli/self_test.py | 1 - anvio/cli/setup_cazymes.py | 1 - anvio/cli/setup_interacdome.py | 1 - anvio/cli/setup_kegg_data.py | 1 - anvio/cli/setup_modelseed_database.py | 1 - anvio/cli/setup_ncbi_cogs.py | 1 - anvio/cli/setup_pdb_database.py | 1 - anvio/cli/setup_pfams.py | 1 - anvio/cli/setup_scg_taxonomy.py | 1 - anvio/cli/setup_trna_taxonomy.py | 1 - anvio/cli/setup_user_modules.py | 1 - anvio/cli/show_collections_and_bins.py | 1 - anvio/cli/show_misc_data.py | 1 - anvio/cli/snvs_to_interactive.py | 1 - anvio/cli/split.py | 1 - anvio/cli/summarize.py | 1 - anvio/cli/summarize_blitz.py | 1 - anvio/cli/tabulate.py | 1 - anvio/cli/tabulate_trnaseq.py | 1 - anvio/cli/transpose_matrix.py | 1 - anvio/cli/trnaseq.py | 1 - anvio/cli/update_db_description.py | 1 - anvio/cli/update_structure_database.py | 1 - anvio/cli/variability_to_vcf.py | 1 - anvio/clustering.py | 1 - anvio/clusteringconfuguration.py | 1 - anvio/codonusage.py | 1 - anvio/cogs.py | 1 - anvio/completeness.py | 1 - anvio/constants.py | 1 - anvio/contigops.py | 1 - anvio/data/SSMs/__init__.py | 1 - anvio/db.py | 1 - anvio/dbinfo.py | 1 - anvio/dbops.py | 1 - anvio/dictio.py | 1 - anvio/docs/__init__.py | 1 - anvio/drivers/MODELLER.py | 1 - anvio/drivers/binsanity.py | 1 - anvio/drivers/blast.py | 1 - anvio/drivers/concoct.py | 1 - anvio/drivers/dastool.py | 1 - anvio/drivers/diamond.py | 1 - anvio/drivers/emapper.py | 1 - anvio/drivers/famsa.py | 1 - anvio/drivers/fastani.py | 1 - anvio/drivers/fasttree.py | 1 - anvio/drivers/hmmer.py | 1 - anvio/drivers/maxbin2.py | 1 - anvio/drivers/mcl.py | 1 - anvio/drivers/metabat2.py | 1 - anvio/drivers/muscle.py | 1 - anvio/drivers/prodigal.py | 1 - anvio/drivers/pyani.py | 1 - anvio/drivers/pyrodigal.py | 1 - anvio/drivers/sourmash.py | 1 - anvio/drivers/trnscan_se.py | 1 - anvio/errors.py | 1 - anvio/fastalib.py | 1 - anvio/filesnpaths.py | 1 - anvio/genecalling.py | 1 - anvio/genomedescriptions.py | 1 - anvio/genomereorientation.py | 1 - anvio/genomesimilarity.py | 1 - anvio/genomestorage.py | 1 - anvio/hmmops.py | 1 - anvio/hmmopswrapper.py | 1 - anvio/homogeneityindex.py | 1 - anvio/interacdome.py | 1 - anvio/interactive.py | 1 - anvio/inversions.py | 1 - anvio/keggmapping.py | 1 - anvio/kgml.py | 1 - anvio/kmers.py | 1 - anvio/learning.py | 1 - anvio/mcgclassifier.py | 1 - anvio/mcgops.py | 1 - anvio/merger.py | 1 - anvio/metabolicexchanges.py | 1 - anvio/metabolism/algorithms.py | 1 - anvio/metabolism/dbaccess.py | 1 - anvio/metabolism/estimate.py | 1 - anvio/metapanops.py | 1 - anvio/migrations/__init__.py | 1 - anvio/migrations/config/v0_to_v1.py | 1 - anvio/migrations/config/v1_to_v2.py | 1 - anvio/migrations/config/v2_to_v3.py | 1 - anvio/migrations/config/v3_to_v4.py | 1 - anvio/migrations/config/v4_to_v5.py | 1 - anvio/migrations/contigs/v10_to_v11.py | 1 - anvio/migrations/contigs/v11_to_v12.py | 1 - anvio/migrations/contigs/v12_to_v13.py | 1 - anvio/migrations/contigs/v13_to_v14.py | 1 - anvio/migrations/contigs/v14_to_v15.py | 1 - anvio/migrations/contigs/v15_to_v16.py | 1 - anvio/migrations/contigs/v16_to_v17.py | 1 - anvio/migrations/contigs/v17_to_v18.py | 1 - anvio/migrations/contigs/v18_to_v19.py | 1 - anvio/migrations/contigs/v19_to_v20.py | 1 - anvio/migrations/contigs/v20_to_v21.py | 1 - anvio/migrations/contigs/v21_to_v22.py | 1 - anvio/migrations/contigs/v22_to_v23.py | 1 - anvio/migrations/contigs/v23_to_v24.py | 1 - anvio/migrations/contigs/v5_to_v6.py | 1 - anvio/migrations/contigs/v6_to_v7.py | 1 - anvio/migrations/contigs/v7_to_v8.py | 1 - anvio/migrations/contigs/v8_to_v9.py | 1 - anvio/migrations/contigs/v9_to_v10.py | 1 - anvio/migrations/genes/v4_to_v5.py | 1 - anvio/migrations/genes/v5_to_v6.py | 1 - anvio/migrations/genomestorage/v3_to_v4.py | 1 - anvio/migrations/genomestorage/v4_to_v5.py | 1 - anvio/migrations/genomestorage/v5_to_v6.py | 1 - anvio/migrations/genomestorage/v6_to_v7.py | 1 - anvio/migrations/genomestorage/v7_to_v8.py | 1 - anvio/migrations/modules/v1_to_v2.py | 1 - anvio/migrations/modules/v2_to_v3.py | 1 - anvio/migrations/modules/v3_to_v4.py | 1 - anvio/migrations/pan/v10_to_v11.py | 1 - anvio/migrations/pan/v11_to_v12.py | 1 - anvio/migrations/pan/v12_to_v13.py | 1 - anvio/migrations/pan/v13_to_v14.py | 1 - anvio/migrations/pan/v14_to_v15.py | 1 - anvio/migrations/pan/v15_to_v16.py | 1 - anvio/migrations/pan/v16_to_v17.py | 1 - anvio/migrations/pan/v17_to_v18.py | 1 - anvio/migrations/pan/v18_to_v19.py | 1 - anvio/migrations/pan/v19_to_v20.py | 1 - anvio/migrations/pan/v20_to_v21.py | 1 - anvio/migrations/pan/v4_to_v5.py | 1 - anvio/migrations/pan/v5_to_v6.py | 1 - anvio/migrations/pan/v6_to_v7.py | 1 - anvio/migrations/pan/v7_to_v8.py | 1 - anvio/migrations/pan/v8_to_v9.py | 1 - anvio/migrations/pan/v9_to_v10.py | 1 - anvio/migrations/profile/v13_to_v14.py | 1 - anvio/migrations/profile/v14_to_v15.py | 1 - anvio/migrations/profile/v15_to_v16.py | 1 - anvio/migrations/profile/v16_to_v17.py | 1 - anvio/migrations/profile/v17_to_v18.py | 1 - anvio/migrations/profile/v18_to_v19.py | 1 - anvio/migrations/profile/v19_to_v20.py | 1 - anvio/migrations/profile/v20_to_v21.py | 1 - anvio/migrations/profile/v21_to_v22.py | 1 - anvio/migrations/profile/v22_to_v23.py | 1 - anvio/migrations/profile/v23_to_v24.py | 1 - anvio/migrations/profile/v24_to_v25.py | 1 - anvio/migrations/profile/v25_to_v26.py | 1 - anvio/migrations/profile/v26_to_v27.py | 1 - anvio/migrations/profile/v27_to_v28.py | 1 - anvio/migrations/profile/v28_to_v29.py | 1 - anvio/migrations/profile/v29_to_v30.py | 1 - anvio/migrations/profile/v30_to_v31.py | 1 - anvio/migrations/profile/v31_to_v32.py | 1 - anvio/migrations/profile/v32_to_v33.py | 1 - anvio/migrations/profile/v33_to_v34.py | 1 - anvio/migrations/profile/v34_to_v35.py | 1 - anvio/migrations/profile/v35_to_v36.py | 1 - anvio/migrations/profile/v36_to_v37.py | 1 - anvio/migrations/profile/v37_to_v38.py | 1 - anvio/migrations/profile/v38_to_v39.py | 1 - anvio/migrations/profile/v39_to_v40.py | 1 - anvio/migrations/profile/v40_to_v41.py | 1 - anvio/migrations/profile/v41_to_v42.py | 1 - anvio/migrations/structure/v1_to_v2.py | 1 - anvio/migrations/trnaseq/v1_to_v2.py | 1 - anvio/panops.py | 1 - anvio/parsers/__init__.py | 1 - anvio/parsers/agnostos.py | 1 - anvio/parsers/base.py | 1 - anvio/parsers/centrifuge.py | 1 - anvio/parsers/defaultmatrix.py | 1 - anvio/parsers/hmmer.py | 1 - anvio/parsers/hmmscan.py | 1 - anvio/parsers/interproscan.py | 1 - anvio/parsers/kaiju.py | 1 - anvio/parsers/krakenuniq.py | 1 - anvio/pfam.py | 1 - anvio/profiler.py | 1 - anvio/programs.py | 1 - anvio/programsearch.py | 1 - anvio/reactionnetwork.py | 1 - anvio/samplesops.py | 1 - anvio/scgdomainclassifier.py | 1 - anvio/sequence.py | 1 - anvio/sequencefeatures.py | 1 - anvio/serverAPI.py | 1 - anvio/sge.py | 1 - anvio/splitter.py | 1 - anvio/structureops.py | 1 - anvio/summarizer.py | 1 - anvio/summaryhtml.py | 1 - anvio/synteny.py | 1 - anvio/tables/__init__.py | 1 - anvio/tables/codonfrequencies.py | 1 - anvio/tables/collections.py | 1 - anvio/tables/contigsplitinfo.py | 1 - anvio/tables/genecalls.py | 1 - anvio/tables/geneclusters.py | 1 - anvio/tables/genefunctions.py | 1 - anvio/tables/genelevelcoverages.py | 1 - anvio/tables/hmmhits.py | 1 - anvio/tables/indels.py | 1 - anvio/tables/kmers.py | 1 - anvio/tables/miscdata.py | 1 - anvio/tables/ntpositions.py | 1 - anvio/tables/scgtaxonomy.py | 1 - anvio/tables/states.py | 1 - anvio/tables/tableops.py | 1 - anvio/tables/taxonomy.py | 1 - anvio/tables/trnahits.py | 1 - anvio/tables/trnataxonomy.py | 1 - anvio/tables/variability.py | 1 - anvio/tables/views.py | 1 - anvio/taxonomyops/__init__.py | 1 - anvio/taxonomyops/scg.py | 1 - anvio/taxonomyops/trna.py | 1 - anvio/terminal.py | 1 - anvio/tests/run_component_tests_for_reaction_network | 1 - anvio/tests/unit/test_anvi_thread.py | 1 - anvio/tests/unit/test_homogeneityindex.py | 1 - anvio/tests/unit/test_palindrome.py | 1 - anvio/tests/unit/utils/test_split_fasta.py | 1 - anvio/threadingops.py | 1 - anvio/trnaidentifier.py | 1 - anvio/trnaseq.py | 1 - anvio/ttycolors.py | 1 - anvio/utils.py | 1 - anvio/variability.py | 1 - anvio/variabilityops.py | 1 - anvio/workflows/__init__.py | 1 - anvio/workflows/contigs/__init__.py | 1 - anvio/workflows/ecophylo/__init__.py | 1 - anvio/workflows/metagenomics/__init__.py | 1 - anvio/workflows/pangenomics/__init__.py | 1 - anvio/workflows/phylogenomics/__init__.py | 1 - anvio/workflows/sra_download/__init__.py | 1 - anvio/workflows/trnaseq/__init__.py | 1 - 403 files changed, 403 deletions(-) diff --git a/anvio/__init__.py b/anvio/__init__.py index 1683132512..b133e8a1f2 100644 --- a/anvio/__init__.py +++ b/anvio/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Lots of under-the-rug, operational garbage in here. Run. Run away.""" diff --git a/anvio/agglomeration.py b/anvio/agglomeration.py index 249a403d3d..e0542e4320 100644 --- a/anvio/agglomeration.py +++ b/anvio/agglomeration.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import gc import os diff --git a/anvio/argparse.py b/anvio/argparse.py index 1cc8c595f8..4fa68b2d69 100755 --- a/anvio/argparse.py +++ b/anvio/argparse.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Overloading Python argparse for anvi'o purposes""" diff --git a/anvio/artifacts/samples_txt.py b/anvio/artifacts/samples_txt.py index a18824c977..1fb325417e 100644 --- a/anvio/artifacts/samples_txt.py +++ b/anvio/artifacts/samples_txt.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import os diff --git a/anvio/authors.py b/anvio/authors.py index ba50df23d6..dae03d0605 100644 --- a/anvio/authors.py +++ b/anvio/authors.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """A library to process anvi'o authors file""" diff --git a/anvio/auxiliarydataops.py b/anvio/auxiliarydataops.py index e97f6a30b3..a3921c5a47 100644 --- a/anvio/auxiliarydataops.py +++ b/anvio/auxiliarydataops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Module to deal with HDF5 files""" diff --git a/anvio/bamops.py b/anvio/bamops.py index 50b5dcd93e..51e3877383 100644 --- a/anvio/bamops.py +++ b/anvio/bamops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Classes for anything BAM-related""" diff --git a/anvio/bottleroutes.py b/anvio/bottleroutes.py index f81eb1a844..755124b03d 100644 --- a/anvio/bottleroutes.py +++ b/anvio/bottleroutes.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Common routes for bottle web server. diff --git a/anvio/cazymes.py b/anvio/cazymes.py index 6d1a5b621c..a188f8153a 100644 --- a/anvio/cazymes.py +++ b/anvio/cazymes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """This file contains CAZyme related classes.""" import os diff --git a/anvio/ccollections.py b/anvio/ccollections.py index f6372b3e40..ec8b1443d7 100644 --- a/anvio/ccollections.py +++ b/anvio/ccollections.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Implements the collections class (the file name has an extra 'c' to avoid diff --git a/anvio/cli/add_default_collection.py b/anvio/cli/add_default_collection.py index 28e9dd53e1..101d1514d1 100755 --- a/anvio/cli/add_default_collection.py +++ b/anvio/cli/add_default_collection.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Adds a DEAFULT collection with EVERYTHING in it into a pan or profile database.""" import sys diff --git a/anvio/cli/analyze_synteny.py b/anvio/cli/analyze_synteny.py index 765cdff675..f141425207 100755 --- a/anvio/cli/analyze_synteny.py +++ b/anvio/cli/analyze_synteny.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """anvi-analyze-synteny ... let's extract some order from this chaos! What do we say to loci that appear to have no coherent synteny patterns...? diff --git a/anvio/cli/annotate_fragmented_genes.py b/anvio/cli/annotate_fragmented_genes.py index 23f1c1a2df..e2d1fdadaa 100644 --- a/anvio/cli/annotate_fragmented_genes.py +++ b/anvio/cli/annotate_fragmented_genes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Identify and annotate fragmented genes (pseudogenes) in pangenomes""" import sys diff --git a/anvio/cli/as_markdown.py b/anvio/cli/as_markdown.py index 3de834c03d..9567e8b517 100755 --- a/anvio/cli/as_markdown.py +++ b/anvio/cli/as_markdown.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/augustus_output_to_external_gene_calls.py b/anvio/cli/augustus_output_to_external_gene_calls.py index 8f02f5d653..69e9afc6fa 100755 --- a/anvio/cli/augustus_output_to_external_gene_calls.py +++ b/anvio/cli/augustus_output_to_external_gene_calls.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/checkm_tree_to_interactive.py b/anvio/cli/checkm_tree_to_interactive.py index 89c554685d..e38437a88c 100755 --- a/anvio/cli/checkm_tree_to_interactive.py +++ b/anvio/cli/checkm_tree_to_interactive.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import re import sys diff --git a/anvio/cli/cluster_contigs.py b/anvio/cli/cluster_contigs.py index a9a412f67e..0ffc8ff2fe 100755 --- a/anvio/cli/cluster_contigs.py +++ b/anvio/cli/cluster_contigs.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to run automatic binning algorithms on a merged anvi'o profile""" import os import sys diff --git a/anvio/cli/compute_ani.py b/anvio/cli/compute_ani.py index 4d40f8503e..10cdb3fb99 100755 --- a/anvio/cli/compute_ani.py +++ b/anvio/cli/compute_ani.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/compute_ani_for_fasta.py b/anvio/cli/compute_ani_for_fasta.py index a91408ae41..f5bd21a0ce 100755 --- a/anvio/cli/compute_ani_for_fasta.py +++ b/anvio/cli/compute_ani_for_fasta.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to export run ANI on every contig in a FASTA file.""" import os diff --git a/anvio/cli/compute_bayesian_pan_core.py b/anvio/cli/compute_bayesian_pan_core.py index abe96f6add..d5b943642c 100755 --- a/anvio/cli/compute_bayesian_pan_core.py +++ b/anvio/cli/compute_bayesian_pan_core.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/compute_completeness.py b/anvio/cli/compute_completeness.py index 0280569ee3..6193c33327 100755 --- a/anvio/cli/compute_completeness.py +++ b/anvio/cli/compute_completeness.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/compute_functional_enrichment.py b/anvio/cli/compute_functional_enrichment.py index 72d576fcb1..db1823cb42 100755 --- a/anvio/cli/compute_functional_enrichment.py +++ b/anvio/cli/compute_functional_enrichment.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.errors import ConfigError diff --git a/anvio/cli/compute_functional_enrichment_across_genomes.py b/anvio/cli/compute_functional_enrichment_across_genomes.py index ad689ea54f..a8fcd6fefd 100755 --- a/anvio/cli/compute_functional_enrichment_across_genomes.py +++ b/anvio/cli/compute_functional_enrichment_across_genomes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program that computes function enrichment across genomees""" import os diff --git a/anvio/cli/compute_functional_enrichment_in_pan.py b/anvio/cli/compute_functional_enrichment_in_pan.py index f5a8e9e9b5..627da0a166 100755 --- a/anvio/cli/compute_functional_enrichment_in_pan.py +++ b/anvio/cli/compute_functional_enrichment_in_pan.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program that computes functional enrichment in a pangenome""" import os diff --git a/anvio/cli/compute_gene_cluster_homogeneity.py b/anvio/cli/compute_gene_cluster_homogeneity.py index f23cb9708f..43bfdd4b8b 100755 --- a/anvio/cli/compute_gene_cluster_homogeneity.py +++ b/anvio/cli/compute_gene_cluster_homogeneity.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/compute_genome_similarity.py b/anvio/cli/compute_genome_similarity.py index 44897ebe2b..6d04b10d28 100755 --- a/anvio/cli/compute_genome_similarity.py +++ b/anvio/cli/compute_genome_similarity.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to export a FASTA files from sequence sources and compute genome similarity matrices.""" import sys diff --git a/anvio/cli/compute_metabolic_enrichment.py b/anvio/cli/compute_metabolic_enrichment.py index 326e583f05..46cf51132f 100755 --- a/anvio/cli/compute_metabolic_enrichment.py +++ b/anvio/cli/compute_metabolic_enrichment.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program that computes metabolic enrichment across groups of genomes and metagenomes""" import sys diff --git a/anvio/cli/compute_rarefaction_curves.py b/anvio/cli/compute_rarefaction_curves.py index 84b21a91f0..590c17bf7a 100755 --- a/anvio/cli/compute_rarefaction_curves.py +++ b/anvio/cli/compute_rarefaction_curves.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program that computes rarefaction curves for a given pan-db""" import sys diff --git a/anvio/cli/db_info.py b/anvio/cli/db_info.py index c660b18ffc..57c08f2a27 100755 --- a/anvio/cli/db_info.py +++ b/anvio/cli/db_info.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/delete_collection.py b/anvio/cli/delete_collection.py index 3de1e14515..9a4cffabb0 100755 --- a/anvio/cli/delete_collection.py +++ b/anvio/cli/delete_collection.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/delete_functions.py b/anvio/cli/delete_functions.py index 23eab5423c..05f9c4a6e0 100755 --- a/anvio/cli/delete_functions.py +++ b/anvio/cli/delete_functions.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/delete_hmms.py b/anvio/cli/delete_hmms.py index a3a73cc188..5b86b6354a 100755 --- a/anvio/cli/delete_hmms.py +++ b/anvio/cli/delete_hmms.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/delete_misc_data.py b/anvio/cli/delete_misc_data.py index 7f9b2493fc..450b9df310 100755 --- a/anvio/cli/delete_misc_data.py +++ b/anvio/cli/delete_misc_data.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Remove stuff from misc data tables""" import sys diff --git a/anvio/cli/delete_state.py b/anvio/cli/delete_state.py index 68134791f7..f7fd21a0af 100755 --- a/anvio/cli/delete_state.py +++ b/anvio/cli/delete_state.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/dereplicate_genomes.py b/anvio/cli/dereplicate_genomes.py index 5b3e3937cc..3e3c2d612e 100755 --- a/anvio/cli/dereplicate_genomes.py +++ b/anvio/cli/dereplicate_genomes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to remove replicated genomes from a list of internal and external genome databases or fasta files""" import sys diff --git a/anvio/cli/display_codon_frequencies.py b/anvio/cli/display_codon_frequencies.py index 0a5ca41a89..8a94b7f73f 100644 --- a/anvio/cli/display_codon_frequencies.py +++ b/anvio/cli/display_codon_frequencies.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Get codon or amino acid frequency statistics from genomes, genes, and functions.""" import sys diff --git a/anvio/cli/display_contigs_stats.py b/anvio/cli/display_contigs_stats.py index a3be490a80..a84c905c88 100755 --- a/anvio/cli/display_contigs_stats.py +++ b/anvio/cli/display_contigs_stats.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/display_functions.py b/anvio/cli/display_functions.py index 6755b5224b..7aa8134d4e 100755 --- a/anvio/cli/display_functions.py +++ b/anvio/cli/display_functions.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to display the distribution of functions across genomes.""" import sys diff --git a/anvio/cli/display_metabolism.py b/anvio/cli/display_metabolism.py index 85a16c92ff..4a863c5582 100755 --- a/anvio/cli/display_metabolism.py +++ b/anvio/cli/display_metabolism.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/display_pan.py b/anvio/cli/display_pan.py index 7d97b75ce2..d0b4ac4c7d 100755 --- a/anvio/cli/display_pan.py +++ b/anvio/cli/display_pan.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Entry point to the interactive interface for pan genomes. The massage of the data is being taken care of in the interactive module, diff --git a/anvio/cli/display_structure.py b/anvio/cli/display_structure.py index 619f393bff..c2f10b39b4 100755 --- a/anvio/cli/display_structure.py +++ b/anvio/cli/display_structure.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/draw_kegg_pathways.py b/anvio/cli/draw_kegg_pathways.py index 2a18c93f9d..8387c77710 100755 --- a/anvio/cli/draw_kegg_pathways.py +++ b/anvio/cli/draw_kegg_pathways.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 DESCRIPTION = "Write KEGG pathway map files incorporating data sourced from anvi'o databases" import os diff --git a/anvio/cli/estimate_genome_completeness.py b/anvio/cli/estimate_genome_completeness.py index 999dcc7627..2a9b538093 100755 --- a/anvio/cli/estimate_genome_completeness.py +++ b/anvio/cli/estimate_genome_completeness.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/estimate_genome_size.py b/anvio/cli/estimate_genome_size.py index 9796730bf2..5d57a011a1 100755 --- a/anvio/cli/estimate_genome_size.py +++ b/anvio/cli/estimate_genome_size.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/estimate_genome_taxonomy.py b/anvio/cli/estimate_genome_taxonomy.py index 41034a38b6..0c807788d8 100755 --- a/anvio/cli/estimate_genome_taxonomy.py +++ b/anvio/cli/estimate_genome_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/estimate_metabolic_independence.py b/anvio/cli/estimate_metabolic_independence.py index d8dbf64a97..c65037b421 100755 --- a/anvio/cli/estimate_metabolic_independence.py +++ b/anvio/cli/estimate_metabolic_independence.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/estimate_metabolism.py b/anvio/cli/estimate_metabolism.py index a8a1b260de..10f9e620cd 100755 --- a/anvio/cli/estimate_metabolism.py +++ b/anvio/cli/estimate_metabolism.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/estimate_scg_taxonomy.py b/anvio/cli/estimate_scg_taxonomy.py index d6286ad3bd..a6a66f3d86 100755 --- a/anvio/cli/estimate_scg_taxonomy.py +++ b/anvio/cli/estimate_scg_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/estimate_trna_taxonomy.py b/anvio/cli/estimate_trna_taxonomy.py index 02b9c197b4..5e8734192e 100755 --- a/anvio/cli/estimate_trna_taxonomy.py +++ b/anvio/cli/estimate_trna_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/experimental_organization.py b/anvio/cli/experimental_organization.py index 7b47988913..267f1a816d 100755 --- a/anvio/cli/experimental_organization.py +++ b/anvio/cli/experimental_organization.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/export_collection.py b/anvio/cli/export_collection.py index 2372212188..b20e085bed 100755 --- a/anvio/cli/export_collection.py +++ b/anvio/cli/export_collection.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Gives you back items in a collection. Output files can directly be used by anvi-import-collection""" diff --git a/anvio/cli/export_contigs.py b/anvio/cli/export_contigs.py index eba1086a56..2b3b4f9891 100755 --- a/anvio/cli/export_contigs.py +++ b/anvio/cli/export_contigs.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to export a FASTA file of contigs (or splits) from a contigs database.""" import sys diff --git a/anvio/cli/export_functions.py b/anvio/cli/export_functions.py index 6292f50b93..374542ce83 100755 --- a/anvio/cli/export_functions.py +++ b/anvio/cli/export_functions.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/export_gene_calls.py b/anvio/cli/export_gene_calls.py index 1011f85ccf..a748686cb6 100755 --- a/anvio/cli/export_gene_calls.py +++ b/anvio/cli/export_gene_calls.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import pandas as pd diff --git a/anvio/cli/export_gene_clusters.py b/anvio/cli/export_gene_clusters.py index bbe77253a9..ca22379172 100755 --- a/anvio/cli/export_gene_clusters.py +++ b/anvio/cli/export_gene_clusters.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/export_gene_coverage_and_detection.py b/anvio/cli/export_gene_coverage_and_detection.py index e5892d760d..65f0121762 100755 --- a/anvio/cli/export_gene_coverage_and_detection.py +++ b/anvio/cli/export_gene_coverage_and_detection.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/export_items_order.py b/anvio/cli/export_items_order.py index aeb1296815..27fef4ef77 100755 --- a/anvio/cli/export_items_order.py +++ b/anvio/cli/export_items_order.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to export an items order from an anvi'o database""" import sys diff --git a/anvio/cli/export_locus.py b/anvio/cli/export_locus.py index a08a0abe16..3c472eb044 100755 --- a/anvio/cli/export_locus.py +++ b/anvio/cli/export_locus.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """anvi-export-locus, first of its name, splitter of loci, and generator of mini contigs databases You want to play with it? This is how you could quickly test it: diff --git a/anvio/cli/export_misc_data.py b/anvio/cli/export_misc_data.py index ec9d4aeccf..c40445f616 100755 --- a/anvio/cli/export_misc_data.py +++ b/anvio/cli/export_misc_data.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Export misc data from target tables into TAB-delimited files""" import sys diff --git a/anvio/cli/export_splits_and_coverages.py b/anvio/cli/export_splits_and_coverages.py index 03a87fc337..4b03b9e9f0 100755 --- a/anvio/cli/export_splits_and_coverages.py +++ b/anvio/cli/export_splits_and_coverages.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to export a FASTA file and the coverage table from a merged database. The purpose of this script is to export two critical files for most genome binning diff --git a/anvio/cli/export_splits_taxonomy.py b/anvio/cli/export_splits_taxonomy.py index 57fd2652b4..19fd9d1823 100755 --- a/anvio/cli/export_splits_taxonomy.py +++ b/anvio/cli/export_splits_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Takes a contigs database, and export taxonomy information from it.""" import sys diff --git a/anvio/cli/export_state.py b/anvio/cli/export_state.py index fcb87c7e37..fc43c29cc4 100755 --- a/anvio/cli/export_state.py +++ b/anvio/cli/export_state.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/export_structures.py b/anvio/cli/export_structures.py index bb3e9d88a7..9110ee839f 100755 --- a/anvio/cli/export_structures.py +++ b/anvio/cli/export_structures.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import anvio diff --git a/anvio/cli/export_table.py b/anvio/cli/export_table.py index 19dc34984f..6a06114767 100755 --- a/anvio/cli/export_table.py +++ b/anvio/cli/export_table.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Takes a database and a table name as parameters, stores the content as a TAB-delimited matrix.""" diff --git a/anvio/cli/filter_fasta_by_blast.py b/anvio/cli/filter_fasta_by_blast.py index 758a30e236..070da34497 100755 --- a/anvio/cli/filter_fasta_by_blast.py +++ b/anvio/cli/filter_fasta_by_blast.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import pandas as pd diff --git a/anvio/cli/filter_hmm_hits_table.py b/anvio/cli/filter_hmm_hits_table.py index 7a10247a3a..5d6d81209e 100755 --- a/anvio/cli/filter_hmm_hits_table.py +++ b/anvio/cli/filter_hmm_hits_table.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """ This script removes the hmm_hits table and replaces it with a filtered version. Filtering of hmm_hits diff --git a/anvio/cli/find_misassemblies.py b/anvio/cli/find_misassemblies.py index 5e54739048..8ce8b8bae7 100755 --- a/anvio/cli/find_misassemblies.py +++ b/anvio/cli/find_misassemblies.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 -*- import sys import anvio diff --git a/anvio/cli/fix_homopolymer_indels.py b/anvio/cli/fix_homopolymer_indels.py index 371281e06b..2859d065ef 100755 --- a/anvio/cli/fix_homopolymer_indels.py +++ b/anvio/cli/fix_homopolymer_indels.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/gen_CPR_classifier.py b/anvio/cli/gen_CPR_classifier.py index 8355fe6ba5..615b2f4faa 100755 --- a/anvio/cli/gen_CPR_classifier.py +++ b/anvio/cli/gen_CPR_classifier.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import random diff --git a/anvio/cli/gen_contigs_database.py b/anvio/cli/gen_contigs_database.py index 6f62d6f2bf..ab861dff54 100755 --- a/anvio/cli/gen_contigs_database.py +++ b/anvio/cli/gen_contigs_database.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/gen_defense_finder_models_to_hmm_directory.py b/anvio/cli/gen_defense_finder_models_to_hmm_directory.py index cf3fdd40bc..7b5421d795 100755 --- a/anvio/cli/gen_defense_finder_models_to_hmm_directory.py +++ b/anvio/cli/gen_defense_finder_models_to_hmm_directory.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/gen_distribution_of_genes_in_a_bin.py b/anvio/cli/gen_distribution_of_genes_in_a_bin.py index 04b83f5adc..2b2e86bd13 100755 --- a/anvio/cli/gen_distribution_of_genes_in_a_bin.py +++ b/anvio/cli/gen_distribution_of_genes_in_a_bin.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import numpy as numpy diff --git a/anvio/cli/gen_fixation_index_matrix.py b/anvio/cli/gen_fixation_index_matrix.py index 71cbf82748..3b54b203bf 100755 --- a/anvio/cli/gen_fixation_index_matrix.py +++ b/anvio/cli/gen_fixation_index_matrix.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Fetches information from the variable positions table""" import sys diff --git a/anvio/cli/gen_function_matrix_across_genomes.py b/anvio/cli/gen_function_matrix_across_genomes.py index 4be6084d1a..e9841048b3 100755 --- a/anvio/cli/gen_function_matrix_across_genomes.py +++ b/anvio/cli/gen_function_matrix_across_genomes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program that uses AggregateFunctions class to generate human-readable output for functions across genomes.""" import os diff --git a/anvio/cli/gen_functions_per_group_stats_output.py b/anvio/cli/gen_functions_per_group_stats_output.py index 3057d4bf1b..5adacd611c 100755 --- a/anvio/cli/gen_functions_per_group_stats_output.py +++ b/anvio/cli/gen_functions_per_group_stats_output.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to generate a functions across groups stats output.""" import sys diff --git a/anvio/cli/gen_gene_consensus_sequences.py b/anvio/cli/gen_gene_consensus_sequences.py index a91dd36ba9..550d62c7cc 100755 --- a/anvio/cli/gen_gene_consensus_sequences.py +++ b/anvio/cli/gen_gene_consensus_sequences.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Collapses variation for a given list of gene caller ids""" import sys diff --git a/anvio/cli/gen_gene_level_stats_databases.py b/anvio/cli/gen_gene_level_stats_databases.py index 311091a5ee..e21d7f1ee0 100755 --- a/anvio/cli/gen_gene_level_stats_databases.py +++ b/anvio/cli/gen_gene_level_stats_databases.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to generate genes databases all at once""" import os diff --git a/anvio/cli/gen_genomes_file.py b/anvio/cli/gen_genomes_file.py index 0ebf77db12..a6b7a270fe 100755 --- a/anvio/cli/gen_genomes_file.py +++ b/anvio/cli/gen_genomes_file.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to generate external or internal genomes files""" diff --git a/anvio/cli/gen_genomes_storage.py b/anvio/cli/gen_genomes_storage.py index 134605a6c0..c0c6e52c15 100755 --- a/anvio/cli/gen_genomes_storage.py +++ b/anvio/cli/gen_genomes_storage.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Generator of genome storages""" import sys diff --git a/anvio/cli/gen_help_pages.py b/anvio/cli/gen_help_pages.py index 9a1bc24d87..5d39b5c28f 100755 --- a/anvio/cli/gen_help_pages.py +++ b/anvio/cli/gen_help_pages.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/gen_hmm_hits_matrix_across_genomes.py b/anvio/cli/gen_hmm_hits_matrix_across_genomes.py index a82ef2e7ce..7f2f491704 100755 --- a/anvio/cli/gen_hmm_hits_matrix_across_genomes.py +++ b/anvio/cli/gen_hmm_hits_matrix_across_genomes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/gen_network.py b/anvio/cli/gen_network.py index b682091254..8eabf4a6c7 100755 --- a/anvio/cli/gen_network.py +++ b/anvio/cli/gen_network.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/gen_phylogenomic_tree.py b/anvio/cli/gen_phylogenomic_tree.py index 080b73e8ac..28d13d0668 100755 --- a/anvio/cli/gen_phylogenomic_tree.py +++ b/anvio/cli/gen_phylogenomic_tree.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Generate phylogenomic tree from aligment file""" import os diff --git a/anvio/cli/gen_programs_network.py b/anvio/cli/gen_programs_network.py index d8d41c4a82..f3bb2cd3b9 100755 --- a/anvio/cli/gen_programs_network.py +++ b/anvio/cli/gen_programs_network.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/gen_programs_vignette.py b/anvio/cli/gen_programs_vignette.py index 698c7ccb9c..1604ac9e00 100755 --- a/anvio/cli/gen_programs_vignette.py +++ b/anvio/cli/gen_programs_vignette.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/gen_pseudo_paired_reads_from_fastq.py b/anvio/cli/gen_pseudo_paired_reads_from_fastq.py index 9b1e364a32..57ee61c82e 100755 --- a/anvio/cli/gen_pseudo_paired_reads_from_fastq.py +++ b/anvio/cli/gen_pseudo_paired_reads_from_fastq.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/gen_reads.py b/anvio/cli/gen_reads.py index b16126e2a7..33e7b7d41b 100644 --- a/anvio/cli/gen_reads.py +++ b/anvio/cli/gen_reads.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/gen_scg_domain_classifier.py b/anvio/cli/gen_scg_domain_classifier.py index f9b3220b20..ea46474504 100755 --- a/anvio/cli/gen_scg_domain_classifier.py +++ b/anvio/cli/gen_scg_domain_classifier.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 # pylint: disable=line-too-long """ diff --git a/anvio/cli/gen_short_reads.py b/anvio/cli/gen_short_reads.py index ea1e80fe56..b494fa19dc 100755 --- a/anvio/cli/gen_short_reads.py +++ b/anvio/cli/gen_short_reads.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import random diff --git a/anvio/cli/gen_structure_database.py b/anvio/cli/gen_structure_database.py index 72cc209a8e..7383f747e7 100755 --- a/anvio/cli/gen_structure_database.py +++ b/anvio/cli/gen_structure_database.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/cli/gen_user_module_file.py b/anvio/cli/gen_user_module_file.py index cb74fc8149..3d57d63c57 100755 --- a/anvio/cli/gen_user_module_file.py +++ b/anvio/cli/gen_user_module_file.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """ This script converts a file with a list of KOs (one KO per line) into a modules file. The file should be tab-delimited and contain 3 columns: the KO identifier, the orthology, and the annotation source. If annotation source is KOfam, the orthology diff --git a/anvio/cli/gen_variability_network.py b/anvio/cli/gen_variability_network.py index ae6ec0807e..b5210356bd 100755 --- a/anvio/cli/gen_variability_network.py +++ b/anvio/cli/gen_variability_network.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Creates a network file for a given variability profile output""" import sys diff --git a/anvio/cli/gen_variability_profile.py b/anvio/cli/gen_variability_profile.py index 5d05abfa2d..efd48bf5cd 100755 --- a/anvio/cli/gen_variability_profile.py +++ b/anvio/cli/gen_variability_profile.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Fetches information from the variable positions table""" import sys diff --git a/anvio/cli/get_aa_counts.py b/anvio/cli/get_aa_counts.py index 9bba446f26..a457682f15 100755 --- a/anvio/cli/get_aa_counts.py +++ b/anvio/cli/get_aa_counts.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Return counts of AAs in bins, contigs, or gene caller ids""" import sys diff --git a/anvio/cli/get_codon_frequencies.py b/anvio/cli/get_codon_frequencies.py index 832ea29fff..ddd5d20ff4 100755 --- a/anvio/cli/get_codon_frequencies.py +++ b/anvio/cli/get_codon_frequencies.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Get codon or amino acid frequency statistics from genomes, genes, and functions.""" import sys diff --git a/anvio/cli/get_codon_usage_bias.py b/anvio/cli/get_codon_usage_bias.py index 87e0f59e04..322bfed811 100755 --- a/anvio/cli/get_codon_usage_bias.py +++ b/anvio/cli/get_codon_usage_bias.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Get codon usage bias (CUB) of genes and functions.""" diff --git a/anvio/cli/get_collection_info.py b/anvio/cli/get_collection_info.py index 04d087fd7e..c477ba18cc 100755 --- a/anvio/cli/get_collection_info.py +++ b/anvio/cli/get_collection_info.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/get_coverage_from_bam.py b/anvio/cli/get_coverage_from_bam.py index 966ce6a3a8..67e7f848ec 100755 --- a/anvio/cli/get_coverage_from_bam.py +++ b/anvio/cli/get_coverage_from_bam.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import numpy as np diff --git a/anvio/cli/get_hmm_hits_per_gene_call.py b/anvio/cli/get_hmm_hits_per_gene_call.py index fd4f9bb54b..dca01b2d64 100755 --- a/anvio/cli/get_hmm_hits_per_gene_call.py +++ b/anvio/cli/get_hmm_hits_per_gene_call.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/get_metabolic_model_file.py b/anvio/cli/get_metabolic_model_file.py index 6fdb9eb840..f8320dfe60 100755 --- a/anvio/cli/get_metabolic_model_file.py +++ b/anvio/cli/get_metabolic_model_file.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 DESCRIPTION = """This program exports a metabolic reaction network to a file suitable for flux balance analysis.""" from sys import exit diff --git a/anvio/cli/get_pn_ps_ratio.py b/anvio/cli/get_pn_ps_ratio.py index 8992124194..231e0ad41e 100755 --- a/anvio/cli/get_pn_ps_ratio.py +++ b/anvio/cli/get_pn_ps_ratio.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """ Citations: doi:10.1126/science.aaz9642, doi:10.1038/nature11711 """ diff --git a/anvio/cli/get_sequences_for_gene_calls.py b/anvio/cli/get_sequences_for_gene_calls.py index 41250c020e..41f0e97661 100755 --- a/anvio/cli/get_sequences_for_gene_calls.py +++ b/anvio/cli/get_sequences_for_gene_calls.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Returns sequences for a given list of gene caller ids""" import sys diff --git a/anvio/cli/get_sequences_for_gene_clusters.py b/anvio/cli/get_sequences_for_gene_clusters.py index 258baccb1c..e0a897d2cf 100755 --- a/anvio/cli/get_sequences_for_gene_clusters.py +++ b/anvio/cli/get_sequences_for_gene_clusters.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Export aligned sequences from anvi'o pan genomes""" import os diff --git a/anvio/cli/get_sequences_for_hmm_hits.py b/anvio/cli/get_sequences_for_hmm_hits.py index f8b99020c2..2005ad5963 100755 --- a/anvio/cli/get_sequences_for_hmm_hits.py +++ b/anvio/cli/get_sequences_for_hmm_hits.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Get sequences for all HMM hits in a given bin. This program takes a profile database, a collection ID, and a bin name, and an diff --git a/anvio/cli/get_short_reads_from_bam.py b/anvio/cli/get_short_reads_from_bam.py index a7a028c2f3..b2e5dd1649 100755 --- a/anvio/cli/get_short_reads_from_bam.py +++ b/anvio/cli/get_short_reads_from_bam.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A client to access short reads in BAM files. diff --git a/anvio/cli/get_short_reads_mapping_to_a_gene.py b/anvio/cli/get_short_reads_mapping_to_a_gene.py index 4dbe248e0b..0d50c02a69 100755 --- a/anvio/cli/get_short_reads_mapping_to_a_gene.py +++ b/anvio/cli/get_short_reads_mapping_to_a_gene.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Return short reads from BAM files mapping to gene.""" diff --git a/anvio/cli/get_split_coverages.py b/anvio/cli/get_split_coverages.py index a89dd3b412..6e71a9f5d6 100755 --- a/anvio/cli/get_split_coverages.py +++ b/anvio/cli/get_split_coverages.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to export coverage values across samples of a given split in an anvi'o contigs db""" import sys diff --git a/anvio/cli/get_tlen_dist_from_bam.py b/anvio/cli/get_tlen_dist_from_bam.py index ee48c7820b..1880f4a52b 100755 --- a/anvio/cli/get_tlen_dist_from_bam.py +++ b/anvio/cli/get_tlen_dist_from_bam.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/hmm_to_hmm_directory.py b/anvio/cli/hmm_to_hmm_directory.py index 42dffb74f1..acc8d260fb 100755 --- a/anvio/cli/hmm_to_hmm_directory.py +++ b/anvio/cli/hmm_to_hmm_directory.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/import_collection.py b/anvio/cli/import_collection.py index bf2c396416..246e839a27 100755 --- a/anvio/cli/import_collection.py +++ b/anvio/cli/import_collection.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to import collections (and their colors)""" import sys diff --git a/anvio/cli/import_functions.py b/anvio/cli/import_functions.py index 205aeded81..be73985245 100755 --- a/anvio/cli/import_functions.py +++ b/anvio/cli/import_functions.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/import_items_order.py b/anvio/cli/import_items_order.py index fed206c250..deded21d1f 100755 --- a/anvio/cli/import_items_order.py +++ b/anvio/cli/import_items_order.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to import an items order into an anvi'o database""" import sys diff --git a/anvio/cli/import_metabolite_profile.py b/anvio/cli/import_metabolite_profile.py index 63ed609656..a5e36ab3b1 100755 --- a/anvio/cli/import_metabolite_profile.py +++ b/anvio/cli/import_metabolite_profile.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 DESCRIPTION = """This program imports metabolite abundance data and stores it in a profile database.""" import pandas as pd diff --git a/anvio/cli/import_misc_data.py b/anvio/cli/import_misc_data.py index 6450be52ff..148e6525cf 100755 --- a/anvio/cli/import_misc_data.py +++ b/anvio/cli/import_misc_data.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Populate misc data tables""" import sys diff --git a/anvio/cli/import_protein_profile.py b/anvio/cli/import_protein_profile.py index bfa7881603..778a149bcf 100755 --- a/anvio/cli/import_protein_profile.py +++ b/anvio/cli/import_protein_profile.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 DESCRIPTION = """This program imports protein abundance data into a profile database.""" import pandas as pd diff --git a/anvio/cli/import_state.py b/anvio/cli/import_state.py index 2fb197ffd1..a832cac3cd 100755 --- a/anvio/cli/import_state.py +++ b/anvio/cli/import_state.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/import_taxonomy_for_genes.py b/anvio/cli/import_taxonomy_for_genes.py index af7a574e3c..e45aa5333e 100755 --- a/anvio/cli/import_taxonomy_for_genes.py +++ b/anvio/cli/import_taxonomy_for_genes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/import_taxonomy_for_layers.py b/anvio/cli/import_taxonomy_for_layers.py index c8d19a6810..f27b0532f1 100755 --- a/anvio/cli/import_taxonomy_for_layers.py +++ b/anvio/cli/import_taxonomy_for_layers.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys from anvio.argparse import ArgumentParser diff --git a/anvio/cli/init_bam.py b/anvio/cli/init_bam.py index 0e9fb65476..e85c068bf9 100755 --- a/anvio/cli/init_bam.py +++ b/anvio/cli/init_bam.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/inspect.py b/anvio/cli/inspect.py index 5a7077fb1a..a31a5aaeb8 100755 --- a/anvio/cli/inspect.py +++ b/anvio/cli/inspect.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """This program runs inspect page directly""" import sys diff --git a/anvio/cli/interactive.py b/anvio/cli/interactive.py index 3309578dcc..4c23e2c008 100755 --- a/anvio/cli/interactive.py +++ b/anvio/cli/interactive.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Entry point to the interactive interface. The massage of the data is being taken care of in the interactive module, diff --git a/anvio/cli/matrix_to_newick.py b/anvio/cli/matrix_to_newick.py index 836dfa65c5..fee9fa9c3b 100755 --- a/anvio/cli/matrix_to_newick.py +++ b/anvio/cli/matrix_to_newick.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/mcg_classifier.py b/anvio/cli/mcg_classifier.py index 0a455982cb..a6f0a3094c 100755 --- a/anvio/cli/mcg_classifier.py +++ b/anvio/cli/mcg_classifier.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 # pylint: disable=line-too-long import sys diff --git a/anvio/cli/merge.py b/anvio/cli/merge.py index b8824c141a..43a16a2372 100755 --- a/anvio/cli/merge.py +++ b/anvio/cli/merge.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Script to merge multiple profiles.""" import sys diff --git a/anvio/cli/merge_bins.py b/anvio/cli/merge_bins.py index 6b7bddec07..222d0811d5 100755 --- a/anvio/cli/merge_bins.py +++ b/anvio/cli/merge_bins.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Allows you to merge multiple bins in a collection""" import sys diff --git a/anvio/cli/merge_collections.py b/anvio/cli/merge_collections.py index 2ea247de0e..e912df331a 100755 --- a/anvio/cli/merge_collections.py +++ b/anvio/cli/merge_collections.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to merge multiple binning results into a single additional data file""" diff --git a/anvio/cli/merge_trnaseq.py b/anvio/cli/merge_trnaseq.py index 850b05e0b1..66abe6a311 100755 --- a/anvio/cli/merge_trnaseq.py +++ b/anvio/cli/merge_trnaseq.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/meta_pan_genome.py b/anvio/cli/meta_pan_genome.py index c01d42b851..a93957c00c 100755 --- a/anvio/cli/meta_pan_genome.py +++ b/anvio/cli/meta_pan_genome.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Entering anvi'o metapangenomic workflow""" import sys diff --git a/anvio/cli/migrate.py b/anvio/cli/migrate.py index db92867683..3157e38292 100755 --- a/anvio/cli/migrate.py +++ b/anvio/cli/migrate.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/oligotype_linkmers.py b/anvio/cli/oligotype_linkmers.py index 2bf66a9161..11bdaaee73 100755 --- a/anvio/cli/oligotype_linkmers.py +++ b/anvio/cli/oligotype_linkmers.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Oligotyping analysis of the linkmer reports.""" diff --git a/anvio/cli/pan_genome.py b/anvio/cli/pan_genome.py index 64179926da..ff943680e2 100755 --- a/anvio/cli/pan_genome.py +++ b/anvio/cli/pan_genome.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A DIAMOND and MCL-based pangenome workflow""" import sys diff --git a/anvio/cli/permute_trnaseq_seeds.py b/anvio/cli/permute_trnaseq_seeds.py index b58ddcc838..5e7d3d20fd 100755 --- a/anvio/cli/permute_trnaseq_seeds.py +++ b/anvio/cli/permute_trnaseq_seeds.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/pfam_accessions_to_hmms_directory.py b/anvio/cli/pfam_accessions_to_hmms_directory.py index 99d25a0fcb..0c59fb589d 100755 --- a/anvio/cli/pfam_accessions_to_hmms_directory.py +++ b/anvio/cli/pfam_accessions_to_hmms_directory.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/plot_trnaseq.py b/anvio/cli/plot_trnaseq.py index 730856c4a4..32ba3e9208 100755 --- a/anvio/cli/plot_trnaseq.py +++ b/anvio/cli/plot_trnaseq.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Plot coverage and modification data from flexible groups of tRNA-seq seeds""" import sys diff --git a/anvio/cli/predict_CPR_genomes.py b/anvio/cli/predict_CPR_genomes.py index 45ed84c6ba..dba388f462 100755 --- a/anvio/cli/predict_CPR_genomes.py +++ b/anvio/cli/predict_CPR_genomes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/predict_metabolic_exchanges.py b/anvio/cli/predict_metabolic_exchanges.py index c02bb12869..607760c5f4 100755 --- a/anvio/cli/predict_metabolic_exchanges.py +++ b/anvio/cli/predict_metabolic_exchanges.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import anvio diff --git a/anvio/cli/process_genbank.py b/anvio/cli/process_genbank.py index 7b1f9c9981..948187439b 100755 --- a/anvio/cli/process_genbank.py +++ b/anvio/cli/process_genbank.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/process_genbank_metadata.py b/anvio/cli/process_genbank_metadata.py index 0d3a71fb74..5553d674fb 100755 --- a/anvio/cli/process_genbank_metadata.py +++ b/anvio/cli/process_genbank_metadata.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/profile.py b/anvio/cli/profile.py index fa0838f451..a44dd123e6 100755 --- a/anvio/cli/profile.py +++ b/anvio/cli/profile.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/cli/profile_blitz.py b/anvio/cli/profile_blitz.py index c10151ddb0..68e7f9a167 100755 --- a/anvio/cli/profile_blitz.py +++ b/anvio/cli/profile_blitz.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/push.py b/anvio/cli/push.py index 83dd0ffc84..aa061e349a 100755 --- a/anvio/cli/push.py +++ b/anvio/cli/push.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to 'push' analyses to anvi'server. Takes multiple files in, sends them to the server.""" diff --git a/anvio/cli/reaction_network.py b/anvio/cli/reaction_network.py index 6beb82863d..d6c0012c82 100755 --- a/anvio/cli/reaction_network.py +++ b/anvio/cli/reaction_network.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 DESCRIPTION = """This program generates a metabolic reaction network in an anvi'o contigs or pan database""" import sys diff --git a/anvio/cli/refine.py b/anvio/cli/refine.py index 370467f5fb..465a08eaa5 100755 --- a/anvio/cli/refine.py +++ b/anvio/cli/refine.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Further analyze one or more bins in a collection. This is especially useful when there are one or more highly contaminated diff --git a/anvio/cli/reformat_bam.py b/anvio/cli/reformat_bam.py index 06a0ee7801..7f89344775 100755 --- a/anvio/cli/reformat_bam.py +++ b/anvio/cli/reformat_bam.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/reformat_fasta.py b/anvio/cli/reformat_fasta.py index 0efacfaf4c..3ee8927ac4 100755 --- a/anvio/cli/reformat_fasta.py +++ b/anvio/cli/reformat_fasta.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import math diff --git a/anvio/cli/rename_bins.py b/anvio/cli/rename_bins.py index a5480ad372..193df3d538 100755 --- a/anvio/cli/rename_bins.py +++ b/anvio/cli/rename_bins.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import copy diff --git a/anvio/cli/reorient_genomes.py b/anvio/cli/reorient_genomes.py index 283b56c522..dbb859ca2c 100644 --- a/anvio/cli/reorient_genomes.py +++ b/anvio/cli/reorient_genomes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# coding: utf-8 import sys diff --git a/anvio/cli/report_circularity.py b/anvio/cli/report_circularity.py index a9f07b5819..f27c857bad 100644 --- a/anvio/cli/report_circularity.py +++ b/anvio/cli/report_circularity.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/report_inversions.py b/anvio/cli/report_inversions.py index 0a66e3dee6..f603c0a5ab 100755 --- a/anvio/cli/report_inversions.py +++ b/anvio/cli/report_inversions.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/report_linkmers.py b/anvio/cli/report_linkmers.py index c4283e380a..9e7f1764be 100755 --- a/anvio/cli/report_linkmers.py +++ b/anvio/cli/report_linkmers.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """The client for LinkMers class. diff --git a/anvio/cli/run_cazymes.py b/anvio/cli/run_cazymes.py index 702e912a00..c26e0094d4 100755 --- a/anvio/cli/run_cazymes.py +++ b/anvio/cli/run_cazymes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/run_eggnog_mapper.py b/anvio/cli/run_eggnog_mapper.py index 0426ddea7c..ccc98526b4 100755 --- a/anvio/cli/run_eggnog_mapper.py +++ b/anvio/cli/run_eggnog_mapper.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import shutil diff --git a/anvio/cli/run_hmms.py b/anvio/cli/run_hmms.py index 663afb3296..0ceb444fa4 100755 --- a/anvio/cli/run_hmms.py +++ b/anvio/cli/run_hmms.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/run_interacdome.py b/anvio/cli/run_interacdome.py index b76e616934..8fd119b76b 100755 --- a/anvio/cli/run_interacdome.py +++ b/anvio/cli/run_interacdome.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/run_kegg_kofams.py b/anvio/cli/run_kegg_kofams.py index 7c011404e3..06542d9ef2 100755 --- a/anvio/cli/run_kegg_kofams.py +++ b/anvio/cli/run_kegg_kofams.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/run_ncbi_cogs.py b/anvio/cli/run_ncbi_cogs.py index 62bb460f38..efe6d29d85 100755 --- a/anvio/cli/run_ncbi_cogs.py +++ b/anvio/cli/run_ncbi_cogs.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/run_pfams.py b/anvio/cli/run_pfams.py index 79d69ac64d..50ea099901 100755 --- a/anvio/cli/run_pfams.py +++ b/anvio/cli/run_pfams.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/run_scg_taxonomy.py b/anvio/cli/run_scg_taxonomy.py index e7c0516289..c8c90b4a7f 100755 --- a/anvio/cli/run_scg_taxonomy.py +++ b/anvio/cli/run_scg_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/run_trna_taxonomy.py b/anvio/cli/run_trna_taxonomy.py index 4b5f95ef76..c1c8380a0d 100755 --- a/anvio/cli/run_trna_taxonomy.py +++ b/anvio/cli/run_trna_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/run_workflow.py b/anvio/cli/run_workflow.py index a3dd1d0375..ecb4486c37 100755 --- a/anvio/cli/run_workflow.py +++ b/anvio/cli/run_workflow.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/scan_trnas.py b/anvio/cli/scan_trnas.py index dbd26b905e..5fa804ff70 100755 --- a/anvio/cli/scan_trnas.py +++ b/anvio/cli/scan_trnas.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/search_functions.py b/anvio/cli/search_functions.py index d80b241c85..7873969b52 100755 --- a/anvio/cli/search_functions.py +++ b/anvio/cli/search_functions.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Searches contigs database for a given function""" import sys diff --git a/anvio/cli/search_palindromes.py b/anvio/cli/search_palindromes.py index 70440772fe..e70bec8b31 100755 --- a/anvio/cli/search_palindromes.py +++ b/anvio/cli/search_palindromes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A program to find palindromes in sequences.""" import sys diff --git a/anvio/cli/search_primers.py b/anvio/cli/search_primers.py index 165ce319b9..6e0f925e6c 100755 --- a/anvio/cli/search_primers.py +++ b/anvio/cli/search_primers.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/search_sequence_motifs.py b/anvio/cli/search_sequence_motifs.py index ee429b35a9..2cc47d2d49 100755 --- a/anvio/cli/search_sequence_motifs.py +++ b/anvio/cli/search_sequence_motifs.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import re import sys diff --git a/anvio/cli/self_test.py b/anvio/cli/self_test.py index 2c9c6e3162..c191798c5c 100755 --- a/anvio/cli/self_test.py +++ b/anvio/cli/self_test.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/cli/setup_cazymes.py b/anvio/cli/setup_cazymes.py index f265cf9264..75c0b5ddb9 100755 --- a/anvio/cli/setup_cazymes.py +++ b/anvio/cli/setup_cazymes.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/setup_interacdome.py b/anvio/cli/setup_interacdome.py index bb8866c9f7..a8bd456244 100755 --- a/anvio/cli/setup_interacdome.py +++ b/anvio/cli/setup_interacdome.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/setup_kegg_data.py b/anvio/cli/setup_kegg_data.py index 2d254b4def..9b919d92e7 100755 --- a/anvio/cli/setup_kegg_data.py +++ b/anvio/cli/setup_kegg_data.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/cli/setup_modelseed_database.py b/anvio/cli/setup_modelseed_database.py index 9ae511a7f7..06a2901cf4 100755 --- a/anvio/cli/setup_modelseed_database.py +++ b/anvio/cli/setup_modelseed_database.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 DESCRIPTION = """This program downloads and sets up the ModelSEED Biochemistry database.""" import os diff --git a/anvio/cli/setup_ncbi_cogs.py b/anvio/cli/setup_ncbi_cogs.py index e8918ca8fe..25c7a2206b 100755 --- a/anvio/cli/setup_ncbi_cogs.py +++ b/anvio/cli/setup_ncbi_cogs.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/setup_pdb_database.py b/anvio/cli/setup_pdb_database.py index 662a090f59..536327fd2d 100755 --- a/anvio/cli/setup_pdb_database.py +++ b/anvio/cli/setup_pdb_database.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import anvio diff --git a/anvio/cli/setup_pfams.py b/anvio/cli/setup_pfams.py index f1d7960c09..7274d6b334 100755 --- a/anvio/cli/setup_pfams.py +++ b/anvio/cli/setup_pfams.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/setup_scg_taxonomy.py b/anvio/cli/setup_scg_taxonomy.py index c68be3f74d..7c86a5e8ff 100755 --- a/anvio/cli/setup_scg_taxonomy.py +++ b/anvio/cli/setup_scg_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/setup_trna_taxonomy.py b/anvio/cli/setup_trna_taxonomy.py index 1523f8c46a..4192375e96 100755 --- a/anvio/cli/setup_trna_taxonomy.py +++ b/anvio/cli/setup_trna_taxonomy.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/setup_user_modules.py b/anvio/cli/setup_user_modules.py index 8293afa0fc..63184b5123 100755 --- a/anvio/cli/setup_user_modules.py +++ b/anvio/cli/setup_user_modules.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/show_collections_and_bins.py b/anvio/cli/show_collections_and_bins.py index 0b26c5e1d0..f8b05b954a 100755 --- a/anvio/cli/show_collections_and_bins.py +++ b/anvio/cli/show_collections_and_bins.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Takes an anvi'o profile or pan database and returns a quick text summary of bins and collections found in it.""" diff --git a/anvio/cli/show_misc_data.py b/anvio/cli/show_misc_data.py index 8d90c64fc9..ead01ece55 100755 --- a/anvio/cli/show_misc_data.py +++ b/anvio/cli/show_misc_data.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """List misc data keys in pan or profile databases""" import sys diff --git a/anvio/cli/snvs_to_interactive.py b/anvio/cli/snvs_to_interactive.py index 64bc38793f..6fbcc25d59 100755 --- a/anvio/cli/snvs_to_interactive.py +++ b/anvio/cli/snvs_to_interactive.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import random diff --git a/anvio/cli/split.py b/anvio/cli/split.py index 819222aa35..83c164653e 100755 --- a/anvio/cli/split.py +++ b/anvio/cli/split.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Split an anvi'o profile into smaller pieces.""" import sys diff --git a/anvio/cli/summarize.py b/anvio/cli/summarize.py index 1d35eb24d9..c4fb5c6a73 100755 --- a/anvio/cli/summarize.py +++ b/anvio/cli/summarize.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Generate summary output from anvi'o datbases""" import os diff --git a/anvio/cli/summarize_blitz.py b/anvio/cli/summarize_blitz.py index 44832b05b7..c39f13b751 100755 --- a/anvio/cli/summarize_blitz.py +++ b/anvio/cli/summarize_blitz.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Script to quickly summarize many single profiles.""" import sys diff --git a/anvio/cli/tabulate.py b/anvio/cli/tabulate.py index bc3160ddad..d80eb2d707 100755 --- a/anvio/cli/tabulate.py +++ b/anvio/cli/tabulate.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/tabulate_trnaseq.py b/anvio/cli/tabulate_trnaseq.py index c2dcf774b3..516e8d6776 100755 --- a/anvio/cli/tabulate_trnaseq.py +++ b/anvio/cli/tabulate_trnaseq.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Tabulate data on tRNA seeds from a set of tRNA-seq samples""" diff --git a/anvio/cli/transpose_matrix.py b/anvio/cli/transpose_matrix.py index b64e35c4a0..bf32b80c35 100755 --- a/anvio/cli/transpose_matrix.py +++ b/anvio/cli/transpose_matrix.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys diff --git a/anvio/cli/trnaseq.py b/anvio/cli/trnaseq.py index 328eeb87cd..62c6723059 100755 --- a/anvio/cli/trnaseq.py +++ b/anvio/cli/trnaseq.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """De novo prediction of tRNAs and their properties from a single tRNA-seq library""" import sys diff --git a/anvio/cli/update_db_description.py b/anvio/cli/update_db_description.py index 6f3f92c97c..f4617d7be2 100755 --- a/anvio/cli/update_db_description.py +++ b/anvio/cli/update_db_description.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """A script to upgrade the description in an anvi'o db""" import sys diff --git a/anvio/cli/update_structure_database.py b/anvio/cli/update_structure_database.py index 0925d0370f..7aff7b0d31 100755 --- a/anvio/cli/update_structure_database.py +++ b/anvio/cli/update_structure_database.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/cli/variability_to_vcf.py b/anvio/cli/variability_to_vcf.py index 83905fcff6..0444d8bf8a 100755 --- a/anvio/cli/variability_to_vcf.py +++ b/anvio/cli/variability_to_vcf.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """ Converts anvi'o variability output to VCF """ diff --git a/anvio/clustering.py b/anvio/clustering.py index 8c9d8aa44c..25b2f17658 100644 --- a/anvio/clustering.py +++ b/anvio/clustering.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Clustering operations and helper functions""" diff --git a/anvio/clusteringconfuguration.py b/anvio/clusteringconfuguration.py index e79ffdae0c..bb5cfe822f 100644 --- a/anvio/clusteringconfuguration.py +++ b/anvio/clusteringconfuguration.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # pylint: disable=line-too-long """To make sense of config files for mixed clustering""" diff --git a/anvio/codonusage.py b/anvio/codonusage.py index 1d9108b630..97512eb781 100644 --- a/anvio/codonusage.py +++ b/anvio/codonusage.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Module for codon usage analyses at the levels of genes, groups of genes, and genomes""" diff --git a/anvio/cogs.py b/anvio/cogs.py index df45f68246..725803c838 100644 --- a/anvio/cogs.py +++ b/anvio/cogs.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Making sense of COGs diff --git a/anvio/completeness.py b/anvio/completeness.py index 908d3ac319..783e38ddca 100644 --- a/anvio/completeness.py +++ b/anvio/completeness.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ diff --git a/anvio/constants.py b/anvio/constants.py index 0e7e8ae0de..ce25a09477 100644 --- a/anvio/constants.py +++ b/anvio/constants.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # pylint: disable=line-too-long import os diff --git a/anvio/contigops.py b/anvio/contigops.py index b3527209fe..43cda8c7bc 100644 --- a/anvio/contigops.py +++ b/anvio/contigops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Classes and functions for handling, storing, and retrieving atomic data from contigs and splits. Also includes classes to deal with external diff --git a/anvio/data/SSMs/__init__.py b/anvio/data/SSMs/__init__.py index 81a6e7c29b..0a41cc9527 100644 --- a/anvio/data/SSMs/__init__.py +++ b/anvio/data/SSMs/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Gather data from SSMs""" diff --git a/anvio/db.py b/anvio/db.py index 532fabd260..a7f92bcf56 100644 --- a/anvio/db.py +++ b/anvio/db.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Low-level db operations. diff --git a/anvio/dbinfo.py b/anvio/dbinfo.py index e7ef0014e0..7c0b3113b8 100644 --- a/anvio/dbinfo.py +++ b/anvio/dbinfo.py @@ -1,5 +1,4 @@ #! /usr/bin/env python -# -*- coding: utf-8 """A module of classes to keep track of anvi'o databases The module includes to major classes: DBInfo, and FindAnvioDBs. diff --git a/anvio/dbops.py b/anvio/dbops.py index 3dd48b0f27..d408b12125 100644 --- a/anvio/dbops.py +++ b/anvio/dbops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to create, access, and/or populate contigs, tRNASeq, and profile databases. diff --git a/anvio/dictio.py b/anvio/dictio.py index 50b502ea0b..035b3db8f7 100644 --- a/anvio/dictio.py +++ b/anvio/dictio.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Module to read and write serialized+compressed anvio objects""" diff --git a/anvio/docs/__init__.py b/anvio/docs/__init__.py index dab7256844..5d2dfec247 100644 --- a/anvio/docs/__init__.py +++ b/anvio/docs/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 """Everything about anvi'o workflows and artifacts""" # when defining a new anvi'o workflow, it is essential to document most critical diff --git a/anvio/drivers/MODELLER.py b/anvio/drivers/MODELLER.py index 67c8bd38b4..00747ffa11 100644 --- a/anvio/drivers/MODELLER.py +++ b/anvio/drivers/MODELLER.py @@ -1,4 +1,3 @@ -# coding: utf-8 """ Interface to MODELLER (https://salilab.org/modeller/). """ diff --git a/anvio/drivers/binsanity.py b/anvio/drivers/binsanity.py index 658260b514..45cb3f0a59 100644 --- a/anvio/drivers/binsanity.py +++ b/anvio/drivers/binsanity.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to BinSanity.""" import os import glob diff --git a/anvio/drivers/blast.py b/anvio/drivers/blast.py index a78bbd4c2c..51add7469a 100644 --- a/anvio/drivers/blast.py +++ b/anvio/drivers/blast.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to NCBI's BLAST.""" import os diff --git a/anvio/drivers/concoct.py b/anvio/drivers/concoct.py index 167fc43967..a870541dbe 100644 --- a/anvio/drivers/concoct.py +++ b/anvio/drivers/concoct.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Anvi'o - CONCOCT interface for unsupervised clustering""" import os diff --git a/anvio/drivers/dastool.py b/anvio/drivers/dastool.py index ee4ba00ecf..e967e08657 100644 --- a/anvio/drivers/dastool.py +++ b/anvio/drivers/dastool.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ """ diff --git a/anvio/drivers/diamond.py b/anvio/drivers/diamond.py index 585ff59a46..a201717dc8 100644 --- a/anvio/drivers/diamond.py +++ b/anvio/drivers/diamond.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to Diamond.""" import os diff --git a/anvio/drivers/emapper.py b/anvio/drivers/emapper.py index 632c671a2c..cf9362cded 100644 --- a/anvio/drivers/emapper.py +++ b/anvio/drivers/emapper.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to eggnog-mapper (https://github.com/jhcepas/eggnog-mapper).""" import os diff --git a/anvio/drivers/famsa.py b/anvio/drivers/famsa.py index d1ae90aaea..e02474a041 100644 --- a/anvio/drivers/famsa.py +++ b/anvio/drivers/famsa.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to FAMSA.""" import os diff --git a/anvio/drivers/fastani.py b/anvio/drivers/fastani.py index 3e0e7f879b..3066f9c51e 100644 --- a/anvio/drivers/fastani.py +++ b/anvio/drivers/fastani.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to fastANI.""" import os diff --git a/anvio/drivers/fasttree.py b/anvio/drivers/fasttree.py index 1cb8695c2b..a2e1569f0c 100644 --- a/anvio/drivers/fasttree.py +++ b/anvio/drivers/fasttree.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to FastTree.""" from subprocess import Popen, PIPE diff --git a/anvio/drivers/hmmer.py b/anvio/drivers/hmmer.py index 409f4f6da8..63332d92d1 100644 --- a/anvio/drivers/hmmer.py +++ b/anvio/drivers/hmmer.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to HMMer.""" import os diff --git a/anvio/drivers/maxbin2.py b/anvio/drivers/maxbin2.py index 939258c421..712047233f 100644 --- a/anvio/drivers/maxbin2.py +++ b/anvio/drivers/maxbin2.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to MaxBin2.""" import os import glob diff --git a/anvio/drivers/mcl.py b/anvio/drivers/mcl.py index 08e14d4f33..ea2dbb510e 100644 --- a/anvio/drivers/mcl.py +++ b/anvio/drivers/mcl.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to MCL.""" import os diff --git a/anvio/drivers/metabat2.py b/anvio/drivers/metabat2.py index 82948a283a..063ab9c32b 100644 --- a/anvio/drivers/metabat2.py +++ b/anvio/drivers/metabat2.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to MetaBAT2.""" import os import glob diff --git a/anvio/drivers/muscle.py b/anvio/drivers/muscle.py index 5562e70dd1..4c255aa094 100644 --- a/anvio/drivers/muscle.py +++ b/anvio/drivers/muscle.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to muscle.""" import os diff --git a/anvio/drivers/prodigal.py b/anvio/drivers/prodigal.py index 26bc2bc52d..27764d63cd 100644 --- a/anvio/drivers/prodigal.py +++ b/anvio/drivers/prodigal.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to Prodigal.""" # Note: The Prodigal command will be run in a "mutlithreaded" way even if the user selects only one thread. In other diff --git a/anvio/drivers/pyani.py b/anvio/drivers/pyani.py index 8f54d1dd7b..e55064e9c0 100644 --- a/anvio/drivers/pyani.py +++ b/anvio/drivers/pyani.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to PyANI.""" import os diff --git a/anvio/drivers/pyrodigal.py b/anvio/drivers/pyrodigal.py index b8fe7b4f5d..b1d5bfb4e0 100644 --- a/anvio/drivers/pyrodigal.py +++ b/anvio/drivers/pyrodigal.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface for gene calling that uses `pyrodigal-gv`.""" import copy diff --git a/anvio/drivers/sourmash.py b/anvio/drivers/sourmash.py index 8946ee5474..c03c0e3bad 100644 --- a/anvio/drivers/sourmash.py +++ b/anvio/drivers/sourmash.py @@ -1,4 +1,3 @@ -# coding: utf-8 """Interface to sourmash""" import os diff --git a/anvio/drivers/trnscan_se.py b/anvio/drivers/trnscan_se.py index 29a9797f66..0657d789f4 100644 --- a/anvio/drivers/trnscan_se.py +++ b/anvio/drivers/trnscan_se.py @@ -1,4 +1,3 @@ -# coding: utf-8 """An interface for tRNAScan-SE""" import anvio diff --git a/anvio/errors.py b/anvio/errors.py index 59ef0b0444..51c2dbd5d5 100644 --- a/anvio/errors.py +++ b/anvio/errors.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Exceptions""" diff --git a/anvio/fastalib.py b/anvio/fastalib.py index cd825bea3b..f00ff2482b 100644 --- a/anvio/fastalib.py +++ b/anvio/fastalib.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # pylint: disable=line-too-long # v.140713 """A very lightweight FASTA I/O library""" diff --git a/anvio/filesnpaths.py b/anvio/filesnpaths.py index e8aeda8494..53629c85e7 100644 --- a/anvio/filesnpaths.py +++ b/anvio/filesnpaths.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """File/Path operations""" diff --git a/anvio/genecalling.py b/anvio/genecalling.py index a48f682ff5..13b08d5b94 100644 --- a/anvio/genecalling.py +++ b/anvio/genecalling.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes for gene calling. diff --git a/anvio/genomedescriptions.py b/anvio/genomedescriptions.py index 31dc2c0ff3..e0bb493b29 100644 --- a/anvio/genomedescriptions.py +++ b/anvio/genomedescriptions.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ A module for dealing with genome storages. diff --git a/anvio/genomereorientation.py b/anvio/genomereorientation.py index 4565c3ce29..cc63c5e75c 100644 --- a/anvio/genomereorientation.py +++ b/anvio/genomereorientation.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# coding: utf-8 """Reorient circular genomes to match a reference genome coordinate system.""" import os diff --git a/anvio/genomesimilarity.py b/anvio/genomesimilarity.py index 95cd8a07be..1add55ee48 100644 --- a/anvio/genomesimilarity.py +++ b/anvio/genomesimilarity.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Code for genome similarity calculation""" import os diff --git a/anvio/genomestorage.py b/anvio/genomestorage.py index ecf15937ea..650c97663e 100644 --- a/anvio/genomestorage.py +++ b/anvio/genomestorage.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ A module to dealing with genome storages. diff --git a/anvio/hmmops.py b/anvio/hmmops.py index c1a5ce6d5c..cbb05f4549 100644 --- a/anvio/hmmops.py +++ b/anvio/hmmops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ HMM related operations. diff --git a/anvio/hmmopswrapper.py b/anvio/hmmopswrapper.py index 33941ca8fb..d818669cb7 100644 --- a/anvio/hmmopswrapper.py +++ b/anvio/hmmopswrapper.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ HMM related operations. diff --git a/anvio/homogeneityindex.py b/anvio/homogeneityindex.py index d18a9bea2e..93ea9dc8e8 100644 --- a/anvio/homogeneityindex.py +++ b/anvio/homogeneityindex.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ A class to compute homogeneity indices for a dictionary of gene clusters using a novel algorithm diff --git a/anvio/interacdome.py b/anvio/interacdome.py index 25d63f76d6..908254dc1b 100644 --- a/anvio/interacdome.py +++ b/anvio/interacdome.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Setup and utilize InteracDome. The InteracDome is from Mona Singh's group at Princeton. In brief, they attribute empirical diff --git a/anvio/interactive.py b/anvio/interactive.py index ef7790bde4..39e8f2f3ba 100644 --- a/anvio/interactive.py +++ b/anvio/interactive.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """The module that curates data for the interactive interface""" diff --git a/anvio/inversions.py b/anvio/inversions.py index 10221e1d4d..57aeca849a 100644 --- a/anvio/inversions.py +++ b/anvio/inversions.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """A module to characterize Florian's inversions""" diff --git a/anvio/keggmapping.py b/anvio/keggmapping.py index abb2c66776..bedcd34629 100644 --- a/anvio/keggmapping.py +++ b/anvio/keggmapping.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Make KEGG pathway maps incorporating data sourced from anvi'o databases.""" import os diff --git a/anvio/kgml.py b/anvio/kgml.py index 0ec30eed1a..5f4ac83f62 100644 --- a/anvio/kgml.py +++ b/anvio/kgml.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """ Manipulate KEGG KGML files, which store certain KEGG pathway map data and can be used to create customized map images. diff --git a/anvio/kmers.py b/anvio/kmers.py index a9a22fbaa5..8c7d4327de 100644 --- a/anvio/kmers.py +++ b/anvio/kmers.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Simple KMers class to compute kmer frequecies diff --git a/anvio/learning.py b/anvio/learning.py index 338ccaf4de..eb3df9925f 100644 --- a/anvio/learning.py +++ b/anvio/learning.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """A simple module with classes for learning operations""" diff --git a/anvio/mcgclassifier.py b/anvio/mcgclassifier.py index b362606c8b..0682fa15b8 100644 --- a/anvio/mcgclassifier.py +++ b/anvio/mcgclassifier.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to classify genes based on coverages across metagenomes. diff --git a/anvio/mcgops.py b/anvio/mcgops.py index ae497de92a..24f9e62aa8 100644 --- a/anvio/mcgops.py +++ b/anvio/mcgops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to classify genes based on coverages across metagenomes. diff --git a/anvio/merger.py b/anvio/merger.py index 76771346c0..7856041e19 100644 --- a/anvio/merger.py +++ b/anvio/merger.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """The library to merge multiple profiles. diff --git a/anvio/metabolicexchanges.py b/anvio/metabolicexchanges.py index dcbe1c45ca..91c60a17ea 100644 --- a/anvio/metabolicexchanges.py +++ b/anvio/metabolicexchanges.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """This file contains classes for predicting metabolic exchanges via the reaction network and KGML processing subsystems.""" import os diff --git a/anvio/metabolism/algorithms.py b/anvio/metabolism/algorithms.py index af9010b483..57fff9f5d3 100644 --- a/anvio/metabolism/algorithms.py +++ b/anvio/metabolism/algorithms.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Core estimation algorithms for the metabolism module. NO BD ACCESS FROM HERE.""" import re diff --git a/anvio/metabolism/dbaccess.py b/anvio/metabolism/dbaccess.py index 876e741d51..185da30916 100644 --- a/anvio/metabolism/dbaccess.py +++ b/anvio/metabolism/dbaccess.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Database access and data loading operations for KEGG metabolism estimation.""" import pandas as pd diff --git a/anvio/metabolism/estimate.py b/anvio/metabolism/estimate.py index b045574340..28cca5f590 100644 --- a/anvio/metabolism/estimate.py +++ b/anvio/metabolism/estimate.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Main KEGG metabolism estimator classes.""" import os diff --git a/anvio/metapanops.py b/anvio/metapanops.py index a1d037d454..3fb9c0aeaf 100644 --- a/anvio/metapanops.py +++ b/anvio/metapanops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ The anvi'o metapangenome module. diff --git a/anvio/migrations/__init__.py b/anvio/migrations/__init__.py index 026ee12bea..e8ce369025 100644 --- a/anvio/migrations/__init__.py +++ b/anvio/migrations/__init__.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import importlib diff --git a/anvio/migrations/config/v0_to_v1.py b/anvio/migrations/config/v0_to_v1.py index b4c3b60c2c..ca63b2d217 100644 --- a/anvio/migrations/config/v0_to_v1.py +++ b/anvio/migrations/config/v0_to_v1.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import json diff --git a/anvio/migrations/config/v1_to_v2.py b/anvio/migrations/config/v1_to_v2.py index 4de0b22fe7..a18ffeaef9 100644 --- a/anvio/migrations/config/v1_to_v2.py +++ b/anvio/migrations/config/v1_to_v2.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import json diff --git a/anvio/migrations/config/v2_to_v3.py b/anvio/migrations/config/v2_to_v3.py index e3c09eeb29..6be2048085 100644 --- a/anvio/migrations/config/v2_to_v3.py +++ b/anvio/migrations/config/v2_to_v3.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import json diff --git a/anvio/migrations/config/v3_to_v4.py b/anvio/migrations/config/v3_to_v4.py index 2f6686b274..59de20e252 100644 --- a/anvio/migrations/config/v3_to_v4.py +++ b/anvio/migrations/config/v3_to_v4.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import json diff --git a/anvio/migrations/config/v4_to_v5.py b/anvio/migrations/config/v4_to_v5.py index 63943e3848..0647958469 100644 --- a/anvio/migrations/config/v4_to_v5.py +++ b/anvio/migrations/config/v4_to_v5.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import json diff --git a/anvio/migrations/contigs/v10_to_v11.py b/anvio/migrations/contigs/v10_to_v11.py index 31bdaae30b..d08587c93b 100755 --- a/anvio/migrations/contigs/v10_to_v11.py +++ b/anvio/migrations/contigs/v10_to_v11.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v11_to_v12.py b/anvio/migrations/contigs/v11_to_v12.py index e0e3db000a..0b0dd87a9b 100755 --- a/anvio/migrations/contigs/v11_to_v12.py +++ b/anvio/migrations/contigs/v11_to_v12.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v12_to_v13.py b/anvio/migrations/contigs/v12_to_v13.py index 09734b93fc..1d853fea09 100755 --- a/anvio/migrations/contigs/v12_to_v13.py +++ b/anvio/migrations/contigs/v12_to_v13.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v13_to_v14.py b/anvio/migrations/contigs/v13_to_v14.py index b15abbc659..fd2f3d9f6d 100644 --- a/anvio/migrations/contigs/v13_to_v14.py +++ b/anvio/migrations/contigs/v13_to_v14.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v14_to_v15.py b/anvio/migrations/contigs/v14_to_v15.py index 9d01f8497d..b7087e8f1e 100644 --- a/anvio/migrations/contigs/v14_to_v15.py +++ b/anvio/migrations/contigs/v14_to_v15.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v15_to_v16.py b/anvio/migrations/contigs/v15_to_v16.py index 1698e4a22c..796161bfb2 100644 --- a/anvio/migrations/contigs/v15_to_v16.py +++ b/anvio/migrations/contigs/v15_to_v16.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v16_to_v17.py b/anvio/migrations/contigs/v16_to_v17.py index de90d9edd3..a2ad4217e0 100644 --- a/anvio/migrations/contigs/v16_to_v17.py +++ b/anvio/migrations/contigs/v16_to_v17.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v17_to_v18.py b/anvio/migrations/contigs/v17_to_v18.py index 18fff18121..f9de321840 100755 --- a/anvio/migrations/contigs/v17_to_v18.py +++ b/anvio/migrations/contigs/v17_to_v18.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v18_to_v19.py b/anvio/migrations/contigs/v18_to_v19.py index 27e4d002c7..be745c3f85 100644 --- a/anvio/migrations/contigs/v18_to_v19.py +++ b/anvio/migrations/contigs/v18_to_v19.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v19_to_v20.py b/anvio/migrations/contigs/v19_to_v20.py index 8553b88568..2eb7b78ef4 100644 --- a/anvio/migrations/contigs/v19_to_v20.py +++ b/anvio/migrations/contigs/v19_to_v20.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v20_to_v21.py b/anvio/migrations/contigs/v20_to_v21.py index af942dc0d2..1b048375df 100644 --- a/anvio/migrations/contigs/v20_to_v21.py +++ b/anvio/migrations/contigs/v20_to_v21.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v21_to_v22.py b/anvio/migrations/contigs/v21_to_v22.py index e5c4f29816..8528091f98 100644 --- a/anvio/migrations/contigs/v21_to_v22.py +++ b/anvio/migrations/contigs/v21_to_v22.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v22_to_v23.py b/anvio/migrations/contigs/v22_to_v23.py index 083b238adf..17c7d79370 100644 --- a/anvio/migrations/contigs/v22_to_v23.py +++ b/anvio/migrations/contigs/v22_to_v23.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v23_to_v24.py b/anvio/migrations/contigs/v23_to_v24.py index 81e5288817..99b3c21d1a 100644 --- a/anvio/migrations/contigs/v23_to_v24.py +++ b/anvio/migrations/contigs/v23_to_v24.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/contigs/v5_to_v6.py b/anvio/migrations/contigs/v5_to_v6.py index 5a0d1622b0..c0a7404b42 100755 --- a/anvio/migrations/contigs/v5_to_v6.py +++ b/anvio/migrations/contigs/v5_to_v6.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v6_to_v7.py b/anvio/migrations/contigs/v6_to_v7.py index 1ec909820d..99d2518d25 100755 --- a/anvio/migrations/contigs/v6_to_v7.py +++ b/anvio/migrations/contigs/v6_to_v7.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v7_to_v8.py b/anvio/migrations/contigs/v7_to_v8.py index 1a9ebbf4b9..5dc5995ac4 100755 --- a/anvio/migrations/contigs/v7_to_v8.py +++ b/anvio/migrations/contigs/v7_to_v8.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v8_to_v9.py b/anvio/migrations/contigs/v8_to_v9.py index e06d0a2823..30bec9089c 100755 --- a/anvio/migrations/contigs/v8_to_v9.py +++ b/anvio/migrations/contigs/v8_to_v9.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/contigs/v9_to_v10.py b/anvio/migrations/contigs/v9_to_v10.py index c27f0af41f..8f8387d230 100755 --- a/anvio/migrations/contigs/v9_to_v10.py +++ b/anvio/migrations/contigs/v9_to_v10.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/genes/v4_to_v5.py b/anvio/migrations/genes/v4_to_v5.py index f5fd67420c..976ac5de38 100755 --- a/anvio/migrations/genes/v4_to_v5.py +++ b/anvio/migrations/genes/v4_to_v5.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/genes/v5_to_v6.py b/anvio/migrations/genes/v5_to_v6.py index 2c41051194..b7c4c58c67 100644 --- a/anvio/migrations/genes/v5_to_v6.py +++ b/anvio/migrations/genes/v5_to_v6.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/genomestorage/v3_to_v4.py b/anvio/migrations/genomestorage/v3_to_v4.py index fd97d15517..5d190ef6ed 100755 --- a/anvio/migrations/genomestorage/v3_to_v4.py +++ b/anvio/migrations/genomestorage/v3_to_v4.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/genomestorage/v4_to_v5.py b/anvio/migrations/genomestorage/v4_to_v5.py index 65fbf964f8..65531c0f9a 100755 --- a/anvio/migrations/genomestorage/v4_to_v5.py +++ b/anvio/migrations/genomestorage/v4_to_v5.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/genomestorage/v5_to_v6.py b/anvio/migrations/genomestorage/v5_to_v6.py index 486a62a423..7c9324f06e 100755 --- a/anvio/migrations/genomestorage/v5_to_v6.py +++ b/anvio/migrations/genomestorage/v5_to_v6.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/genomestorage/v6_to_v7.py b/anvio/migrations/genomestorage/v6_to_v7.py index 9cf0c147ff..297f1b9334 100644 --- a/anvio/migrations/genomestorage/v6_to_v7.py +++ b/anvio/migrations/genomestorage/v6_to_v7.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/genomestorage/v7_to_v8.py b/anvio/migrations/genomestorage/v7_to_v8.py index 5d750f46d9..f1a533b643 100644 --- a/anvio/migrations/genomestorage/v7_to_v8.py +++ b/anvio/migrations/genomestorage/v7_to_v8.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Migration script that detects and repairs bytes-string corruption in genomes storage databases that were converted from HDF5 to SQLite via the v4-to-v5 diff --git a/anvio/migrations/modules/v1_to_v2.py b/anvio/migrations/modules/v1_to_v2.py index 63aee97e8b..b4da6d26d3 100755 --- a/anvio/migrations/modules/v1_to_v2.py +++ b/anvio/migrations/modules/v1_to_v2.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/modules/v2_to_v3.py b/anvio/migrations/modules/v2_to_v3.py index ebb1a9e16f..24dded050b 100644 --- a/anvio/migrations/modules/v2_to_v3.py +++ b/anvio/migrations/modules/v2_to_v3.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/modules/v3_to_v4.py b/anvio/migrations/modules/v3_to_v4.py index 6740404d51..ea1950bd6d 100644 --- a/anvio/migrations/modules/v3_to_v4.py +++ b/anvio/migrations/modules/v3_to_v4.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v10_to_v11.py b/anvio/migrations/pan/v10_to_v11.py index 7b9d3250cb..7986f19e10 100755 --- a/anvio/migrations/pan/v10_to_v11.py +++ b/anvio/migrations/pan/v10_to_v11.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v11_to_v12.py b/anvio/migrations/pan/v11_to_v12.py index 61313a0e08..0212b3e344 100755 --- a/anvio/migrations/pan/v11_to_v12.py +++ b/anvio/migrations/pan/v11_to_v12.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v12_to_v13.py b/anvio/migrations/pan/v12_to_v13.py index 926b3c881b..3488523e55 100644 --- a/anvio/migrations/pan/v12_to_v13.py +++ b/anvio/migrations/pan/v12_to_v13.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v13_to_v14.py b/anvio/migrations/pan/v13_to_v14.py index 643301bf45..9882ded3a1 100644 --- a/anvio/migrations/pan/v13_to_v14.py +++ b/anvio/migrations/pan/v13_to_v14.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v14_to_v15.py b/anvio/migrations/pan/v14_to_v15.py index 01893f63db..5ed66c25af 100644 --- a/anvio/migrations/pan/v14_to_v15.py +++ b/anvio/migrations/pan/v14_to_v15.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v15_to_v16.py b/anvio/migrations/pan/v15_to_v16.py index e7492b705e..ceee22a785 100644 --- a/anvio/migrations/pan/v15_to_v16.py +++ b/anvio/migrations/pan/v15_to_v16.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v16_to_v17.py b/anvio/migrations/pan/v16_to_v17.py index e8547be21d..94845c6ec0 100644 --- a/anvio/migrations/pan/v16_to_v17.py +++ b/anvio/migrations/pan/v16_to_v17.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v17_to_v18.py b/anvio/migrations/pan/v17_to_v18.py index 974c4cfbed..e6bf525f88 100644 --- a/anvio/migrations/pan/v17_to_v18.py +++ b/anvio/migrations/pan/v17_to_v18.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v18_to_v19.py b/anvio/migrations/pan/v18_to_v19.py index e41f2f83e1..beb9b32562 100644 --- a/anvio/migrations/pan/v18_to_v19.py +++ b/anvio/migrations/pan/v18_to_v19.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v19_to_v20.py b/anvio/migrations/pan/v19_to_v20.py index a730d60bd5..bb68959fa7 100644 --- a/anvio/migrations/pan/v19_to_v20.py +++ b/anvio/migrations/pan/v19_to_v20.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/pan/v20_to_v21.py b/anvio/migrations/pan/v20_to_v21.py index 188621cbe6..9f33235c5d 100644 --- a/anvio/migrations/pan/v20_to_v21.py +++ b/anvio/migrations/pan/v20_to_v21.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v4_to_v5.py b/anvio/migrations/pan/v4_to_v5.py index ab52dac9e7..a0f5d946b4 100755 --- a/anvio/migrations/pan/v4_to_v5.py +++ b/anvio/migrations/pan/v4_to_v5.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v5_to_v6.py b/anvio/migrations/pan/v5_to_v6.py index 387668756d..e5807dbe9c 100755 --- a/anvio/migrations/pan/v5_to_v6.py +++ b/anvio/migrations/pan/v5_to_v6.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v6_to_v7.py b/anvio/migrations/pan/v6_to_v7.py index cddd0e295b..2c185a449d 100755 --- a/anvio/migrations/pan/v6_to_v7.py +++ b/anvio/migrations/pan/v6_to_v7.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v7_to_v8.py b/anvio/migrations/pan/v7_to_v8.py index c3a95b57c1..57e3844e7e 100755 --- a/anvio/migrations/pan/v7_to_v8.py +++ b/anvio/migrations/pan/v7_to_v8.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/pan/v8_to_v9.py b/anvio/migrations/pan/v8_to_v9.py index 65f105326b..7ab32b1c78 100755 --- a/anvio/migrations/pan/v8_to_v9.py +++ b/anvio/migrations/pan/v8_to_v9.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/pan/v9_to_v10.py b/anvio/migrations/pan/v9_to_v10.py index b03ccccd48..fc712d3e77 100755 --- a/anvio/migrations/pan/v9_to_v10.py +++ b/anvio/migrations/pan/v9_to_v10.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v13_to_v14.py b/anvio/migrations/profile/v13_to_v14.py index c7c4e910df..9e1c7efc8f 100755 --- a/anvio/migrations/profile/v13_to_v14.py +++ b/anvio/migrations/profile/v13_to_v14.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v14_to_v15.py b/anvio/migrations/profile/v14_to_v15.py index 9c09d33c23..2b6afa6598 100755 --- a/anvio/migrations/profile/v14_to_v15.py +++ b/anvio/migrations/profile/v14_to_v15.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/profile/v15_to_v16.py b/anvio/migrations/profile/v15_to_v16.py index 31fe413439..00954494b0 100755 --- a/anvio/migrations/profile/v15_to_v16.py +++ b/anvio/migrations/profile/v15_to_v16.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v16_to_v17.py b/anvio/migrations/profile/v16_to_v17.py index f69f79771e..e8b2885144 100755 --- a/anvio/migrations/profile/v16_to_v17.py +++ b/anvio/migrations/profile/v16_to_v17.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v17_to_v18.py b/anvio/migrations/profile/v17_to_v18.py index be92a0d964..f33074b5af 100755 --- a/anvio/migrations/profile/v17_to_v18.py +++ b/anvio/migrations/profile/v17_to_v18.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v18_to_v19.py b/anvio/migrations/profile/v18_to_v19.py index 364d2e09df..9262741db4 100755 --- a/anvio/migrations/profile/v18_to_v19.py +++ b/anvio/migrations/profile/v18_to_v19.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v19_to_v20.py b/anvio/migrations/profile/v19_to_v20.py index 86b6b9034e..eb0461681b 100755 --- a/anvio/migrations/profile/v19_to_v20.py +++ b/anvio/migrations/profile/v19_to_v20.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v20_to_v21.py b/anvio/migrations/profile/v20_to_v21.py index 543638524e..9d0790babb 100755 --- a/anvio/migrations/profile/v20_to_v21.py +++ b/anvio/migrations/profile/v20_to_v21.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v21_to_v22.py b/anvio/migrations/profile/v21_to_v22.py index cf211013ce..0552906d32 100755 --- a/anvio/migrations/profile/v21_to_v22.py +++ b/anvio/migrations/profile/v21_to_v22.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/profile/v22_to_v23.py b/anvio/migrations/profile/v22_to_v23.py index 4f4e986be5..289b8bdc46 100755 --- a/anvio/migrations/profile/v22_to_v23.py +++ b/anvio/migrations/profile/v22_to_v23.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import sys diff --git a/anvio/migrations/profile/v23_to_v24.py b/anvio/migrations/profile/v23_to_v24.py index 3bd9ca722a..160d11b8e7 100755 --- a/anvio/migrations/profile/v23_to_v24.py +++ b/anvio/migrations/profile/v23_to_v24.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v24_to_v25.py b/anvio/migrations/profile/v24_to_v25.py index 6ad07e9ede..184e120567 100755 --- a/anvio/migrations/profile/v24_to_v25.py +++ b/anvio/migrations/profile/v24_to_v25.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v25_to_v26.py b/anvio/migrations/profile/v25_to_v26.py index 3cdd392cd9..cf9ef14a0b 100755 --- a/anvio/migrations/profile/v25_to_v26.py +++ b/anvio/migrations/profile/v25_to_v26.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v26_to_v27.py b/anvio/migrations/profile/v26_to_v27.py index e187a0531c..8663fdada9 100755 --- a/anvio/migrations/profile/v26_to_v27.py +++ b/anvio/migrations/profile/v26_to_v27.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v27_to_v28.py b/anvio/migrations/profile/v27_to_v28.py index 2d5960d72a..138b7aef60 100755 --- a/anvio/migrations/profile/v27_to_v28.py +++ b/anvio/migrations/profile/v27_to_v28.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v28_to_v29.py b/anvio/migrations/profile/v28_to_v29.py index 4a8fb84349..d258ef5e1d 100755 --- a/anvio/migrations/profile/v28_to_v29.py +++ b/anvio/migrations/profile/v28_to_v29.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v29_to_v30.py b/anvio/migrations/profile/v29_to_v30.py index 7e3acb074f..58f9d5471e 100755 --- a/anvio/migrations/profile/v29_to_v30.py +++ b/anvio/migrations/profile/v29_to_v30.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v30_to_v31.py b/anvio/migrations/profile/v30_to_v31.py index 912dd3aac8..7cff32b3ff 100755 --- a/anvio/migrations/profile/v30_to_v31.py +++ b/anvio/migrations/profile/v30_to_v31.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v31_to_v32.py b/anvio/migrations/profile/v31_to_v32.py index 0f7b076875..2d996f4ca0 100644 --- a/anvio/migrations/profile/v31_to_v32.py +++ b/anvio/migrations/profile/v31_to_v32.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v32_to_v33.py b/anvio/migrations/profile/v32_to_v33.py index 53242bab57..415bf4437c 100644 --- a/anvio/migrations/profile/v32_to_v33.py +++ b/anvio/migrations/profile/v32_to_v33.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v33_to_v34.py b/anvio/migrations/profile/v33_to_v34.py index 0c03b939a3..5f85399d95 100644 --- a/anvio/migrations/profile/v33_to_v34.py +++ b/anvio/migrations/profile/v33_to_v34.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v34_to_v35.py b/anvio/migrations/profile/v34_to_v35.py index e21c3e5957..497a124626 100644 --- a/anvio/migrations/profile/v34_to_v35.py +++ b/anvio/migrations/profile/v34_to_v35.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v35_to_v36.py b/anvio/migrations/profile/v35_to_v36.py index 2f62486c77..3e005d985b 100755 --- a/anvio/migrations/profile/v35_to_v36.py +++ b/anvio/migrations/profile/v35_to_v36.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v36_to_v37.py b/anvio/migrations/profile/v36_to_v37.py index f5cb0765ca..ceae8cd3dc 100755 --- a/anvio/migrations/profile/v36_to_v37.py +++ b/anvio/migrations/profile/v36_to_v37.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v37_to_v38.py b/anvio/migrations/profile/v37_to_v38.py index 3556b7cd79..f22de467cf 100755 --- a/anvio/migrations/profile/v37_to_v38.py +++ b/anvio/migrations/profile/v37_to_v38.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v38_to_v39.py b/anvio/migrations/profile/v38_to_v39.py index b07e2636d8..494d03814f 100644 --- a/anvio/migrations/profile/v38_to_v39.py +++ b/anvio/migrations/profile/v38_to_v39.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v39_to_v40.py b/anvio/migrations/profile/v39_to_v40.py index 5d5a8a1433..13113de381 100644 --- a/anvio/migrations/profile/v39_to_v40.py +++ b/anvio/migrations/profile/v39_to_v40.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/profile/v40_to_v41.py b/anvio/migrations/profile/v40_to_v41.py index 82101ea54c..bf83296269 100644 --- a/anvio/migrations/profile/v40_to_v41.py +++ b/anvio/migrations/profile/v40_to_v41.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Migration script to convert _contigs view tables from split-keyed to contig-keyed. diff --git a/anvio/migrations/profile/v41_to_v42.py b/anvio/migrations/profile/v41_to_v42.py index 66c72c68ed..b86801e243 100644 --- a/anvio/migrations/profile/v41_to_v42.py +++ b/anvio/migrations/profile/v41_to_v42.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """Migration script to remove zero-value rows from view tables into zero_coverage tables. diff --git a/anvio/migrations/structure/v1_to_v2.py b/anvio/migrations/structure/v1_to_v2.py index 4595ad6b38..d057aef090 100644 --- a/anvio/migrations/structure/v1_to_v2.py +++ b/anvio/migrations/structure/v1_to_v2.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import sys import argparse diff --git a/anvio/migrations/trnaseq/v1_to_v2.py b/anvio/migrations/trnaseq/v1_to_v2.py index 11ab559c02..1282cec92c 100644 --- a/anvio/migrations/trnaseq/v1_to_v2.py +++ b/anvio/migrations/trnaseq/v1_to_v2.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import argparse diff --git a/anvio/panops.py b/anvio/panops.py index b4adfb14a4..ffb317f8ee 100644 --- a/anvio/panops.py +++ b/anvio/panops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes for pan operations. diff --git a/anvio/parsers/__init__.py b/anvio/parsers/__init__.py index 1e2e7b79f8..bc56c2a7d9 100644 --- a/anvio/parsers/__init__.py +++ b/anvio/parsers/__init__.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import anvio import anvio.terminal as terminal diff --git a/anvio/parsers/agnostos.py b/anvio/parsers/agnostos.py index f5682d0eb2..3d7c824c5c 100644 --- a/anvio/parsers/agnostos.py +++ b/anvio/parsers/agnostos.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import pandas as pd diff --git a/anvio/parsers/base.py b/anvio/parsers/base.py index 62abb43662..74e208cce1 100644 --- a/anvio/parsers/base.py +++ b/anvio/parsers/base.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 """ Base class for parsers to take care of the boring stuff. """ diff --git a/anvio/parsers/centrifuge.py b/anvio/parsers/centrifuge.py index caf152a7b3..4d10ad6428 100644 --- a/anvio/parsers/centrifuge.py +++ b/anvio/parsers/centrifuge.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 from collections import Counter diff --git a/anvio/parsers/defaultmatrix.py b/anvio/parsers/defaultmatrix.py index 1d66401c16..688d341f72 100644 --- a/anvio/parsers/defaultmatrix.py +++ b/anvio/parsers/defaultmatrix.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import anvio import anvio.terminal as terminal diff --git a/anvio/parsers/hmmer.py b/anvio/parsers/hmmer.py index 87bcb08602..ba68346751 100644 --- a/anvio/parsers/hmmer.py +++ b/anvio/parsers/hmmer.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 """Parser for HMMER's various outputs""" import anvio diff --git a/anvio/parsers/hmmscan.py b/anvio/parsers/hmmscan.py index 5ca4cef795..0c1bf0c482 100644 --- a/anvio/parsers/hmmscan.py +++ b/anvio/parsers/hmmscan.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 """Parser for HMMER's various outputs""" import anvio diff --git a/anvio/parsers/interproscan.py b/anvio/parsers/interproscan.py index 87d07a026e..1d64dd82a6 100644 --- a/anvio/parsers/interproscan.py +++ b/anvio/parsers/interproscan.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import pandas as pd diff --git a/anvio/parsers/kaiju.py b/anvio/parsers/kaiju.py index 4d433201d2..e3a75bfc01 100644 --- a/anvio/parsers/kaiju.py +++ b/anvio/parsers/kaiju.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import os import random diff --git a/anvio/parsers/krakenuniq.py b/anvio/parsers/krakenuniq.py index 60bd99c000..6219dbb9fa 100644 --- a/anvio/parsers/krakenuniq.py +++ b/anvio/parsers/krakenuniq.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 import anvio import anvio.terminal as terminal diff --git a/anvio/pfam.py b/anvio/pfam.py index d53eed82e2..8a453215b1 100644 --- a/anvio/pfam.py +++ b/anvio/pfam.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 """This file contains PfamSetup and Pfam classes.""" import anvio diff --git a/anvio/profiler.py b/anvio/profiler.py index b8b0b8e169..f578ed00f8 100644 --- a/anvio/profiler.py +++ b/anvio/profiler.py @@ -1,4 +1,3 @@ -# coding: utf-8 # pylint: disable=line-too-long """Provides the necessary class to profile BAM files.""" diff --git a/anvio/programs.py b/anvio/programs.py index 5c3e62132a..671a1786d3 100644 --- a/anvio/programs.py +++ b/anvio/programs.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """A library to help anvi'o describe itself""" diff --git a/anvio/programsearch.py b/anvio/programsearch.py index 9f14632588..87267d280f 100644 --- a/anvio/programsearch.py +++ b/anvio/programsearch.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # A library to search anvi'o programs based on keywords or input/output files # see `anvi-help` for its default client diff --git a/anvio/reactionnetwork.py b/anvio/reactionnetwork.py index 78ecc64211..2a45a9e88e 100644 --- a/anvio/reactionnetwork.py +++ b/anvio/reactionnetwork.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Generate, manipulate, and export metabolic reaction networks from gene annotations.""" diff --git a/anvio/samplesops.py b/anvio/samplesops.py index 5ea20ad904..01be832aff 100644 --- a/anvio/samplesops.py +++ b/anvio/samplesops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Module to make sense of samples information and samples order input""" diff --git a/anvio/scgdomainclassifier.py b/anvio/scgdomainclassifier.py index 141d0baa2c..6dd9c938a3 100644 --- a/anvio/scgdomainclassifier.py +++ b/anvio/scgdomainclassifier.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import os diff --git a/anvio/sequence.py b/anvio/sequence.py index 8569151123..a71a845c14 100644 --- a/anvio/sequence.py +++ b/anvio/sequence.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Classes for sequence properties and manipulations""" diff --git a/anvio/sequencefeatures.py b/anvio/sequencefeatures.py index 8e4845c85c..d77b161806 100755 --- a/anvio/sequencefeatures.py +++ b/anvio/sequencefeatures.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Classes to deal with sequence features""" diff --git a/anvio/serverAPI.py b/anvio/serverAPI.py index 21f32638fc..cd1b9c2d8f 100644 --- a/anvio/serverAPI.py +++ b/anvio/serverAPI.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 """A simple anvi'server API.""" import json diff --git a/anvio/sge.py b/anvio/sge.py index 44d4bfa6ff..869546aced 100644 --- a/anvio/sge.py +++ b/anvio/sge.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Module to submit/track jobs for SUN Grid Engine""" diff --git a/anvio/splitter.py b/anvio/splitter.py index 8a64cb2aac..ec88fa9ac7 100644 --- a/anvio/splitter.py +++ b/anvio/splitter.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """The library to split merged profiles into smaller profiles. diff --git a/anvio/structureops.py b/anvio/structureops.py index 7e0e6de3fc..a9fb8a9870 100755 --- a/anvio/structureops.py +++ b/anvio/structureops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Classes to make sense of genes and variability within the context of protein structure""" diff --git a/anvio/summarizer.py b/anvio/summarizer.py index 417947fe65..018802c5ce 100644 --- a/anvio/summarizer.py +++ b/anvio/summarizer.py @@ -1,4 +1,3 @@ -# coding: utf-8 # pylint: disable=line-too-long """Summarizes information for a collection. diff --git a/anvio/summaryhtml.py b/anvio/summaryhtml.py index 639b9f7c3f..e6d36078c7 100644 --- a/anvio/summaryhtml.py +++ b/anvio/summaryhtml.py @@ -1,4 +1,3 @@ -# coding: utf-8 # pylint: disable=line-too-long """Creates an HTML output to act as a front-end for the static summary directory.""" diff --git a/anvio/synteny.py b/anvio/synteny.py index 7604e5e43d..7ac0cd05c4 100644 --- a/anvio/synteny.py +++ b/anvio/synteny.py @@ -1,4 +1,3 @@ -#!/usr/bin/env python # -*- coding: utf-8 # pylint: disable=line-too-long """Classes to work with ngrams of contig functions. diff --git a/anvio/tables/__init__.py b/anvio/tables/__init__.py index e5f16e0746..eaaf2d9593 100644 --- a/anvio/tables/__init__.py +++ b/anvio/tables/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Table schemas for databases.""" diff --git a/anvio/tables/codonfrequencies.py b/anvio/tables/codonfrequencies.py index 2fe014f017..804f582fd4 100755 --- a/anvio/tables/codonfrequencies.py +++ b/anvio/tables/codonfrequencies.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import anvio diff --git a/anvio/tables/collections.py b/anvio/tables/collections.py index 5a39b4cfe8..9bf5608d82 100644 --- a/anvio/tables/collections.py +++ b/anvio/tables/collections.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """TablesForCollections""" diff --git a/anvio/tables/contigsplitinfo.py b/anvio/tables/contigsplitinfo.py index da988e40a8..a4e1ff4eaf 100644 --- a/anvio/tables/contigsplitinfo.py +++ b/anvio/tables/contigsplitinfo.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long diff --git a/anvio/tables/genecalls.py b/anvio/tables/genecalls.py index 13c891b5ab..f79588d5ab 100644 --- a/anvio/tables/genecalls.py +++ b/anvio/tables/genecalls.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import os diff --git a/anvio/tables/geneclusters.py b/anvio/tables/geneclusters.py index 3b57bbca3b..e4eda6debb 100644 --- a/anvio/tables/geneclusters.py +++ b/anvio/tables/geneclusters.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """TablesForCollections""" diff --git a/anvio/tables/genefunctions.py b/anvio/tables/genefunctions.py index 034fbea126..ccab4d7d25 100644 --- a/anvio/tables/genefunctions.py +++ b/anvio/tables/genefunctions.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import anvio diff --git a/anvio/tables/genelevelcoverages.py b/anvio/tables/genelevelcoverages.py index 6bb61cba21..858763cb7e 100644 --- a/anvio/tables/genelevelcoverages.py +++ b/anvio/tables/genelevelcoverages.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import numpy as np diff --git a/anvio/tables/hmmhits.py b/anvio/tables/hmmhits.py index d27477f466..790fc124dc 100644 --- a/anvio/tables/hmmhits.py +++ b/anvio/tables/hmmhits.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import os diff --git a/anvio/tables/indels.py b/anvio/tables/indels.py index 8799ef45d8..022cef3d78 100644 --- a/anvio/tables/indels.py +++ b/anvio/tables/indels.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import anvio diff --git a/anvio/tables/kmers.py b/anvio/tables/kmers.py index 85a38e5336..b9064f3d45 100644 --- a/anvio/tables/kmers.py +++ b/anvio/tables/kmers.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """TablesForCollections""" diff --git a/anvio/tables/miscdata.py b/anvio/tables/miscdata.py index f877ea3825..3a7e54fa28 100644 --- a/anvio/tables/miscdata.py +++ b/anvio/tables/miscdata.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """The fancy additioanl data module""" diff --git a/anvio/tables/ntpositions.py b/anvio/tables/ntpositions.py index ace5f48286..918ee49657 100644 --- a/anvio/tables/ntpositions.py +++ b/anvio/tables/ntpositions.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import numpy diff --git a/anvio/tables/scgtaxonomy.py b/anvio/tables/scgtaxonomy.py index 74c47f7deb..547ded6beb 100644 --- a/anvio/tables/scgtaxonomy.py +++ b/anvio/tables/scgtaxonomy.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import anvio diff --git a/anvio/tables/states.py b/anvio/tables/states.py index 15987fc3b3..56c0f7dc97 100644 --- a/anvio/tables/states.py +++ b/anvio/tables/states.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import datetime diff --git a/anvio/tables/tableops.py b/anvio/tables/tableops.py index 134d41619e..88a0d2b9a7 100755 --- a/anvio/tables/tableops.py +++ b/anvio/tables/tableops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Table schemas for databases.""" diff --git a/anvio/tables/taxonomy.py b/anvio/tables/taxonomy.py index 54ca4c4ba3..4ac031c1b4 100644 --- a/anvio/tables/taxonomy.py +++ b/anvio/tables/taxonomy.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long from collections import Counter diff --git a/anvio/tables/trnahits.py b/anvio/tables/trnahits.py index 145f407c65..6558dcd970 100644 --- a/anvio/tables/trnahits.py +++ b/anvio/tables/trnahits.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ The purpose of this module is to help the dealing with tRNA genes diff --git a/anvio/tables/trnataxonomy.py b/anvio/tables/trnataxonomy.py index 0899725a2c..1fde5c53ce 100644 --- a/anvio/tables/trnataxonomy.py +++ b/anvio/tables/trnataxonomy.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import anvio diff --git a/anvio/tables/variability.py b/anvio/tables/variability.py index 1835b222da..93c1fc0539 100644 --- a/anvio/tables/variability.py +++ b/anvio/tables/variability.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import anvio diff --git a/anvio/tables/views.py b/anvio/tables/views.py index 717417b26b..9b2723736f 100644 --- a/anvio/tables/views.py +++ b/anvio/tables/views.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long import anvio diff --git a/anvio/taxonomyops/__init__.py b/anvio/taxonomyops/__init__.py index c75c99f4d3..6d75307e85 100644 --- a/anvio/taxonomyops/__init__.py +++ b/anvio/taxonomyops/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Common functions and classes for SCG/TRNA taxonomy. diff --git a/anvio/taxonomyops/scg.py b/anvio/taxonomyops/scg.py index 9d3f683707..68cb3788f4 100644 --- a/anvio/taxonomyops/scg.py +++ b/anvio/taxonomyops/scg.py @@ -1,5 +1,4 @@ #!/usr/bin/env python3 -# -*- coding: utf-8 """ Classes to setup remote SCG databases in local, use local databases to affiliate SCGs in anvi'o contigs databases with taxon names, and estimate taxonomy for genomes and metagenomes. diff --git a/anvio/taxonomyops/trna.py b/anvio/taxonomyops/trna.py index 2f24eb42b7..6a8aafa0bc 100644 --- a/anvio/taxonomyops/trna.py +++ b/anvio/taxonomyops/trna.py @@ -1,5 +1,4 @@ #!/usr/bin/env python3 -# -*- coding: utf-8 """ Classes to use local databases for tRNA taxonomy to affiliate tRNA seqeunces in anvi'o databases with taxon names. diff --git a/anvio/terminal.py b/anvio/terminal.py index 31929915d1..fb331e38fa 100644 --- a/anvio/terminal.py +++ b/anvio/terminal.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Relations with the console output, Progress and Run classes""" diff --git a/anvio/tests/run_component_tests_for_reaction_network b/anvio/tests/run_component_tests_for_reaction_network index dd9867f2b4..09a9f0baad 100755 --- a/anvio/tests/run_component_tests_for_reaction_network +++ b/anvio/tests/run_component_tests_for_reaction_network @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 DESCRIPTION = """Run by the shell script of the same name that tests anvi'o reaction networks.""" from argparse import Namespace diff --git a/anvio/tests/unit/test_anvi_thread.py b/anvio/tests/unit/test_anvi_thread.py index 7b542de7c3..19efa0671f 100644 --- a/anvio/tests/unit/test_anvi_thread.py +++ b/anvio/tests/unit/test_anvi_thread.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 """ Unit tests for the AnviThread class. """ diff --git a/anvio/tests/unit/test_homogeneityindex.py b/anvio/tests/unit/test_homogeneityindex.py index 965573be70..2ea2ad6071 100644 --- a/anvio/tests/unit/test_homogeneityindex.py +++ b/anvio/tests/unit/test_homogeneityindex.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Unit tests for the HomogeneityCalculator class. diff --git a/anvio/tests/unit/test_palindrome.py b/anvio/tests/unit/test_palindrome.py index 3a502e8ecf..1cd3396ee6 100644 --- a/anvio/tests/unit/test_palindrome.py +++ b/anvio/tests/unit/test_palindrome.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Tests for Palindromes""" diff --git a/anvio/tests/unit/utils/test_split_fasta.py b/anvio/tests/unit/utils/test_split_fasta.py index a5b43696a1..b3ab82c9a3 100644 --- a/anvio/tests/unit/utils/test_split_fasta.py +++ b/anvio/tests/unit/utils/test_split_fasta.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Unit tests for the split_fasta function. diff --git a/anvio/threadingops.py b/anvio/threadingops.py index c116e2f22f..ba681204ce 100644 --- a/anvio/threadingops.py +++ b/anvio/threadingops.py @@ -1,4 +1,3 @@ -# coding: utf-8 """A namespace for various threading operations. Exports diff --git a/anvio/trnaidentifier.py b/anvio/trnaidentifier.py index e6002c604f..a8b84e16c9 100644 --- a/anvio/trnaidentifier.py +++ b/anvio/trnaidentifier.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """tRNA identification from a nucleotide sequence.""" diff --git a/anvio/trnaseq.py b/anvio/trnaseq.py index c8c8b95cee..60da62de3f 100644 --- a/anvio/trnaseq.py +++ b/anvio/trnaseq.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Library for tRNA-seq dataset operations diff --git a/anvio/ttycolors.py b/anvio/ttycolors.py index dad48ff9ec..126f95a73d 100644 --- a/anvio/ttycolors.py +++ b/anvio/ttycolors.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """TTY colors""" diff --git a/anvio/utils.py b/anvio/utils.py index 9357f2b3ac..58f7b40e55 100644 --- a/anvio/utils.py +++ b/anvio/utils.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Lonely, helper functions that are broadly used and don't fit anywhere""" diff --git a/anvio/variability.py b/anvio/variability.py index 53b6b90c6f..2156e3160b 100644 --- a/anvio/variability.py +++ b/anvio/variability.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Classes to make sense of single nucleotide variation""" diff --git a/anvio/variabilityops.py b/anvio/variabilityops.py index 0fea6def73..801a4ee389 100644 --- a/anvio/variabilityops.py +++ b/anvio/variabilityops.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Classes to make sense of sequence variation""" diff --git a/anvio/workflows/__init__.py b/anvio/workflows/__init__.py index b54ebab55d..e264937cdd 100644 --- a/anvio/workflows/__init__.py +++ b/anvio/workflows/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Helper functions for the anvi'o snakemake workflows""" diff --git a/anvio/workflows/contigs/__init__.py b/anvio/workflows/contigs/__init__.py index 1924122455..4a884940fe 100644 --- a/anvio/workflows/contigs/__init__.py +++ b/anvio/workflows/contigs/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to define and work with anvi'o contigs workflows. diff --git a/anvio/workflows/ecophylo/__init__.py b/anvio/workflows/ecophylo/__init__.py index 6b2e2509c9..575a2007f4 100644 --- a/anvio/workflows/ecophylo/__init__.py +++ b/anvio/workflows/ecophylo/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to define and work with anvi'o ecophylo workflows. """ diff --git a/anvio/workflows/metagenomics/__init__.py b/anvio/workflows/metagenomics/__init__.py index 1e99d86acf..8a72b456b1 100644 --- a/anvio/workflows/metagenomics/__init__.py +++ b/anvio/workflows/metagenomics/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to define and work with anvi'o contigs workflows. diff --git a/anvio/workflows/pangenomics/__init__.py b/anvio/workflows/pangenomics/__init__.py index 7ca8e426a5..545102b496 100644 --- a/anvio/workflows/pangenomics/__init__.py +++ b/anvio/workflows/pangenomics/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to define and work with anvi'o pangenomics workflows. diff --git a/anvio/workflows/phylogenomics/__init__.py b/anvio/workflows/phylogenomics/__init__.py index 5966f01816..1e19a61814 100644 --- a/anvio/workflows/phylogenomics/__init__.py +++ b/anvio/workflows/phylogenomics/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to define and work with anvi'o phylogenomics workflows. diff --git a/anvio/workflows/sra_download/__init__.py b/anvio/workflows/sra_download/__init__.py index bbfd4773df..bfe235fdb6 100644 --- a/anvio/workflows/sra_download/__init__.py +++ b/anvio/workflows/sra_download/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """ Classes to define and work with anvi'o SRA_downloads workflow. """ diff --git a/anvio/workflows/trnaseq/__init__.py b/anvio/workflows/trnaseq/__init__.py index ce317fe51d..f4e6cf95ec 100644 --- a/anvio/workflows/trnaseq/__init__.py +++ b/anvio/workflows/trnaseq/__init__.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 # pylint: disable=line-too-long """Sets up an anvi'o tRNA-seq snakemake workflow."""