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Fixing taxon list read error in concatenate.py

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Katzlab 2024-08-22 11:59:38 -04:00 committed by GitHub
parent 4676ef2b53
commit 41cc1354b3
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1 changed files with 3 additions and 3 deletions
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PTL2/Scripts/concatenate.py
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@ -118,14 +118,14 @@ def remove_paralogs(params):
#Getting a clean list of all target taxa
if type(params.concat_target_taxa) is list:
target_codes = [code.strip() for code in params.concat_target_taxa if code.strip() != '']
elif params.concat_target_taxa != None:
if os.path.isdir(params.concat_target_taxa):
if os.path.isfile(params.concat_target_taxa):
try:
target_codes = [l.strip() for l in open(params.concat_target_taxa).readlines() if l.strip() != '']
except AttributeError:
print('\n\nError: invalid "concat_target_taxa" argument. This must be a comma-separated list of any number of digits/characters to describe focal taxa (e.g. Sr_ci_S OR Am_tu), or a file with the extension .txt containing a list of complete or partial taxon codes. All sequences containing the complete/partial code will be identified as belonging to target taxa.\n\n')
elif params.concat_target_taxa != None:
target_codes = [params.concat_target_taxa]
else:
print('\nERROR: missing --concat_target_taxa argument. When concatenating, you need to give the taxonomic group (sequence prefix), groups, or a file containing a list of groups (multiple prefixes) for which to select sequences to construct a concatenated alignment\n')
exit()