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symlink hsp result if there is only one #410

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symlink hsp result if there is only one #410

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9 changes: 5 additions & 4 deletions picrust2/pipeline.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python

from os import path
from os import path, symlink
import sys
from picrust2.default import (default_ref_dir_bac, default_ref_dir_arc, default_tables_bac,
default_tables_arc, default_pathway_map)
Expand Down Expand Up @@ -370,21 +370,22 @@ def full_pipeline_split(study_fasta,
for pred in predicted_funcs_split:
if func in pred:
combining.append(pred)


out_file = path.join(output_folder, "combined_" + func + "_predicted.tsv.gz")
if len(combining) == 1:
predicted_funcs[func] = predicted_funcs_split[combining[0]]
print("Warning: There was only one file for the function: "+ func + "\n"
"Maybe that's fine if you used custom traits or there were no sequences "
"matching one of the domains.", file=sys.stderr)

os.symlink(predicted_funcs[func], out_file)

elif len(combining) > 2:
sys.exit("More than two files were available for the function: " + func +"\n"
"If you are using your own custom trait files, please check that you "
"have not given the same table more than once for a domain.")

else:
print(combining, predicted_funcs_split)
out_file = path.join(output_folder, "combined_" + func + "_predicted.tsv.gz")
combine_domain_predictions(predicted_funcs_split[combining[0]],
predicted_funcs_split[combining[1]],
out_file,
Expand Down