Aggregate blast results and/or perform MLST for a set of sample sequences vs a given panel of queries.
Searches a given list of blast databases or fasta files for either:
- a panel of one or more sequences (eg resistance genes) from a multifasta query file, or
- the MLST profile for each sample and produces combined output for the dataset.
Similarity is reported as relative coverage, calculated as (sequence identity * query coverage).
With --save_results also outputs the hits for each query sequence in fasta format.
With --do_mutations reports sequence differences (eg. drug resistance mutations) in the form XNY, where X is the reference (subject) residue, N is the position in the reference sequence, and Y is the query residue at this position.
Example: MLST on assembled data from a single sample:
{typewriter.py} --infastapath /path/to/my/sample/contigs.fasta
--outprefix my_mlst_results
--outdir /path/to/outut/directory
--mlst True
--word_size 11
--allelefile /path/to/my/allelefile.tsv
--stfile /path/to/my/STfile.tsv