Funmap doesn't extract files from archive? #3
Description
I'm trying to follow the readme in order to use funmap. Here's my config file
task: 'protein_func'
name: 'Ccrcc_normal'
seed: 42
results_dir: 'results/Ccrcc_normal'
cor_type: 'pearson'
feature_type: 'mr'
n_jobs: 16
start_edge_num: 1000
min_sample_count: 15
max_num_edges: 250000
step_size: 100
lr_cutoff: 50
data_path: 'Ccrcc_normal.tgz'
data_files:
- name: ccrcc_proteomic_normal
type: protein
path: ccrcc_proteomic_normal.tsv
- name: ccrcc_transcript_normal
type: rna
path: ccrcc_transcript_normal.tsv
rp_pairs:
- name: ccrcc_pair_normal
rna: ccrcc_transcript_normal
protein: ccrcc_proteomic_normal
filter_noncoding_genes: True
Ccrcc_normal.tgz contains 2 files:
ccrcc_transcript_normal.tsv
ccrcc_proteomic_normal.tsv
When I run either run or qc it seems like it doesn't actually extract files from archive to tmp_data
funmap qc -c Ccrcc_normal.yaml ====== funmap ======= 2025-10-15 09:30:12,741 - WARNING - "logging.yml" not found. Using basicConfig with custom log files. 2025-10-15 09:30:12,741 - INFO - Running QC... 2025-10-15 09:30:15,618 - INFO - processing ... ccrcc_proteomic_normal Traceback (most recent call last): File "/media/windows/conda/funmap/bin/funmap", line 7, in <module> sys.exit(cli()) ^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/funmap/cli.py", line 53, in qc fig_names = explore_data(cfg, min_sample_count, figure_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/funmap/plotting.py", line 116, in explore_data data_dict, _ = get_data_dict(data_config, min_sample_count) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/funmap/utils.py", line 98, in get_data_dict cur_data = pd.read_csv(os.path.join(tmp_dir, dt['path']), sep='\t', index_col=0, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read parser = TextFileReader(filepath_or_buffer, **kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__ self._engine = self._make_engine(f, self.engine) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine self.handles = get_handle( ^^^^^^^^^^^ File "/media/windows/conda/funmap/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle handle = open( ^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'tmp_data/ccrcc_proteomic_normal.tsv'