iquasere
commented
2 years ago Hi there!
And thank you for your interest in the tool! This is something that escaped the testings, and I will launch a new version tomorrow to fix it! In the mean time, if you want this fixed right away, you can edit the reCOGnizer script with some text editor, and change the line
'f{directory}/cog2ko.tsv', sep='\t', index=False, header=['cog', 'KO'])to
f'{directory}/cog2ko.tsv', sep='\t', index=False, header=['cog', 'KO'])This was a mistake on my part, and I am sorry for it. You can also run which recognizer.py to know which is the right file to edit!
gaworj
Hi, Thank you very much for such amazing tool.
When I try to run recognizer for COG database I encounter such issue:
[1/1] Handling COG identifications grep -E 'K[0-9]{5}$' /media/jang/SSD2/recognizer_resources_dir/protein.info.v11.0.txt | awk '{{if (length($NF) == 6) print $1, $NF}}' awk '{if (length($4) == 7) print $1" "$4}' /media/jang/SSD2/recognizer_resources_dir/COG.mappings.v11.0.txt | sort | join - /media/jang/SSD2/recognizer_resources_dir/string2ko.tsv join: -:13109: is not sorted: 1001530.BACE01000023_gene1 COG5184 join: /media/jang/SSD2/recognizer_resources_dir/string2ko.tsv:61: is not sorted: 264203.ZMO1579 K06889 Traceback (most recent call last): File "/home/jang/anaconda3/envs/deepnog/bin/recognizer.py", line 461, in
main()
File "/home/jang/anaconda3/envs/deepnog/bin/recognizer.py", line 432, in main
report = cog2ko(report, cog2ko=f'{args.resources_directory}/cog2ko.tsv')
File "/home/jang/anaconda3/envs/deepnog/bin/recognizer.py", line 272, in cog2ko
df[['COG', 'KO']].groupby('COG')['KO'].agg([('KO', ','.join)]).reset_index().to_csv(
File "/home/jang/anaconda3/envs/deepnog/lib/python3.9/site-packages/pandas/core/generic.py", line 3466, in to_csv
return DataFrameRenderer(formatter).to_csv(
File "/home/jang/anaconda3/envs/deepnog/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1105, in to_csv
csv_formatter.save()
File "/home/jang/anaconda3/envs/deepnog/lib/python3.9/site-packages/pandas/io/formats/csvs.py", line 237, in save
with get_handle(
File "/home/jang/anaconda3/envs/deepnog/lib/python3.9/site-packages/pandas/io/common.py", line 702, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'f{directory}/cog2ko.tsv'
Any hints?
Bests, Jan