Ignoring GS record with incorrect columns #11
Description
I've encountered this issue when running cath-align-summary on 4.3 stockholms.
Here's the command I used:
(venv) -bash-4.2$ cath-align-summary -d /data/v4_3_0.staging/003.correct_funfam_sto_headers/output.seed_alignments.sto/ -f stockholm --suffix sto --skipempty
`2020-08-07 12:20:10,066 WARNING | ignoring GS record with incorrect columns (<string>:450 "#=GS 1oxgA01/16-27_121-232AC P00766")
2020-08-07 12:20:10,066 WARNING | ignoring GS record with incorrect columns (<string>:478 "#=GS 1k2i101/18-27_121-232AC P00766")
2020-08-07 12:20:10,066 WARNING | ignoring GS record with incorrect columns (<string>:513 "#=GS 1gl1C01/16-27_121-232AC P00766")
2020-08-07 12:20:10,066 WARNING | ignoring GS record with incorrect columns (<string>:520 "#=GS 1gl1B01/16-27_121-232AC P00766")
2020-08-07 12:20:10,066 WARNING | ignoring GS record with incorrect columns (<string>:527 "#=GS 1gl1A01/16-27_121-232AC P00766")
2020-08-07 12:20:10,066 WARNING | ignoring GS record with incorrect columns (<string>:534 "#=GS 1gl0E01/17-27_121-232AC P00766")
2020-08-07 12:20:10,066 WARNING | ignoring GS record with incorrect columns (<string>:576 "#=GS 1gcdA01/16-27_121-232AC P00766")
2020-08-07 12:20:10,067 WARNING | ignoring GS record with incorrect columns (<string>:583 "#=GS 1ex3A01/16-27_121-232AC P00766")
2020-08-07 12:20:10,067 WARNING | ignoring GS record with incorrect columns (<string>:590 "#=GS
1dlkD01/1-12_106-217AC P00766")
2020-08-07 12:20:10,067 WARNING | ignoring GS record with incorrect columns (<string>:597 "#=GS 1dlkB01/1-12_106-217AC P00766")
2020-08-07 12:20:10,067 WARNING | ignoring GS record with incorrect columns (<string>:611 "#=GS 1chgA01/16-27_121-232AC P00766")
2020-08-07 12:20:10,067 WARNING | ignoring GS record with incorrect columns (<string>:618 "#=GS 1cgjE01/16-27_121-232AC P00766")
2020-08-07 12:20:10,067 WARNING | ignoring GS record with incorrect columns (<string>:625 "#=GS 1cgiE01/16-27_121-232AC P00766")
2020-08-07 12:20:10,067 WARNING | ignoring GS record with incorrect columns (<string>:667 "#=GS 1acbE01/16-27_121-232AC P00766")
2020-08-07 12:20:10,089 WARNING | ignoring GS record with incorrect columns (<string>:6 "#=GS 1fujD02/13-109_211-221AC P24158")
2020-08-07 12:20:10,089 WARNING | ignoring GS record with incorrect columns (<string>:8 "#=GS 1fujD02/13-109_211-221DE Myeloblastin")
2020-08-07 12:20:10,089 WARNING | ignoring GS record with incorrect columns (<string>:11 "#=GS 1fujC02/13-109_211-221AC P24158")
2020-08-07 12:20:10,089 WARNING | ignoring GS record with incorrect columns (<string>:13 "#=GS 1fujC02/13-109_211-221DE Myeloblastin")
2020-08-07 12:20:10,089 WARNING | ignoring GS record with incorrect columns (<string>:16 "#=GS 1fujB02/13-109_211-221AC P24158")
2020-08-07 12:20:10,089 WARNING | ignoring GS record with incorrect columns (<string>:18 "#=GS 1fujB02/13-109_211-221DE Myeloblastin")
2020-08-07 12:20:10,089 WARNING | ignoring GS record with incorrect columns (<string>:21 "#=GS 1fujA02/13-109_211-221AC P24158")
2020-08-07 12:20:10,090 WARNING | ignoring GS record with incorrect columns (<string>:23 "#=GS 1fujA02/13-109_211-221DE Myeloblastin")
Traceback (most recent call last):
File "/cath/people2/ucbtnb4/venv/lib64/python3.6/site-packages/cathpy/core/util.py", line 650, in run
aln = self._file_parser(aln_file)
File "/cath/people2/ucbtnb4/venv/lib64/python3.6/site-packages/cathpy/core/align.py", line 1022, in from_stockholm
seq_id, seq_aa = line.split()
ValueError: not enough values to unpack (expected 2, got 1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cath/people2/ucbtnb4/venv/bin/cath-align-summary", line 54, in <module>
entries = aln_sum.run()
File "/cath/people2/ucbtnb4/venv/lib64/python3.6/site-packages/cathpy/core/util.py", line 653, in run
aln_file, self._parser_name.__name__))
AttributeError: 'AlignmentSummaryRunner' object has no attribute '_parser_name'`Can we expect empty stockholm files? What seems to be the problem for this?