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Bugfix paralogs_ks_multi command #75

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Merged
Cecilia-Sensalari merged 1 commit into from
Jan 21, 2026
Merged

Bugfix paralogs_ks_multi command #75

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11 changes: 8 additions & 3 deletions ksrates_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -315,8 +315,9 @@ def paralogs_analyses(config_file, expert, paranome_table, anchors_table, recipr
@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
@click.option("--n-threads", type=int, default=1, help="Number of threads (default: 1)")
@click.option("--custom-recret-gfs", type=click.Path(exists=True), help="User-defined path to MCL-like file containing reciprocally retained GFs (default: paralog_distribution/wgd_species/species_rec_ret_top_2000.mcl.tsv)")
@click.option("--parsed-homology-table", type=click.Path(exists=True), help="User-defined path to parsed homology table ('BPO file') generated by a previous OrthoMCL run")
@click.option("--test", is_flag=True, default=False, help="Flag for test dataset (Default: False)")
def paralogs_ks_multi(config_sources, expert, n_threads, custom_recret_gfs, test):
def paralogs_ks_multi(config_sources, expert, n_threads, custom_recret_gfs, parsed_homology_table, test):
"""
Performs paralog Ks estimation through wgd for all species present in the Newick tree in the configuration file(s) provided as argument.

Expand All @@ -337,6 +338,10 @@ def paralogs_ks_multi(config_sources, expert, n_threads, custom_recret_gfs, test
expert = ""
if custom_recret_gfs:
click.format_filename(custom_recret_gfs)
if parsed_homology_table: # If not provided, it's "None"
click.format_filename(parsed_homology_table)
else:
parsed_homology_table = ""

# Process any provided source of configuration files (either files or directories containing files)
for source in config_sources:
Expand All @@ -345,15 +350,15 @@ def paralogs_ks_multi(config_sources, expert, n_threads, custom_recret_gfs, test
# If configuration source is a file, use it directly to launch the command
if os.path.isfile(source):
click.format_filename(source)
wgd_paralogs(source, expert, n_threads, custom_recret_gfs, test)
wgd_paralogs(source, expert, n_threads, custom_recret_gfs, parsed_homology_table, test)
print("")

# Else if configuration source is a directory, loop through the files thereby contained and use them
elif os.path.isdir(source):
for config_file in os.listdir(source):
config_file = os.path.join(source, config_file)
click.format_filename(config_file)
wgd_paralogs(config_file, expert, n_threads, custom_recret_gfs, test)
wgd_paralogs(config_file, expert, n_threads, custom_recret_gfs, parsed_homology_table, test)
print("")


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