First, thank you for such a nice tool, I am writing a comment more than an error. I am using protein fasta files produced by NCBI's PGAP annotation. In this case, the header of each protein follow the template "gnl|extdb|pgaptmp_XXXXXX" (where X are numbers) plus a variable functional description. The issue comes when running BuildGroups.py, more exactly at hash_fastas(). The error is the following:
Traceback (most recent call last):
File "~/miniconda3/envs/PyParanoid-stable/bin/BuildGroups.py", line 584, in <module>
main()
File "~/miniconda3/envs/PyParanoid-stable/bin/BuildGroups.py", line 555, in main
seqdata, desc, seq_number = hash_fastas()
File "~/miniconda3/envs/PyParanoid-stable/bin/BuildGroups.py", line 213, in hash_fastas
desc[str(seq.id)] = match.group(2)
AttributeError: 'NoneType' object has no attribute 'group'
The execution fails because the regular expression for the variable match produce a NoneType object (Line 237: match = re.search("(description:)(.*)",d)).
I patch the error by correcting the protein fasta header using linux comments:
cd Data/FAA/pep
ls | xargs -I {} sh -c "sed -i 's/gnl|extdb|//g' {}"
Hi everyone,
First, thank you for such a nice tool, I am writing a comment more than an error. I am using protein fasta files produced by NCBI's PGAP annotation. In this case, the header of each protein follow the template "gnl|extdb|pgaptmp_XXXXXX" (where X are numbers) plus a variable functional description. The issue comes when running BuildGroups.py, more exactly at
hash_fastas(). The error is the following:The execution fails because the regular expression for the variable
matchproduce a NoneType object (Line 237:match = re.search("(description:)(.*)",d)).I patch the error by correcting the protein fasta header using linux comments:
I hope it helps! :)