compare_gos.py namedtuple error

[marade]

It looks like the NamedTuple is being incorrectly created?

[06:30:08 ~/GO]$ compare_gos.py --gaf=../blah.gaf -o compare.tab 502S0.tab 805S0.tab 806S0.tab 808S0.tab 810S0.tab
requests.get(http://purl.obolibrary.org/obo/go/go-basic.obo, stream=True)
WROTE: go-basic.obo

go-basic.obo: fmt(1.2) rel(2020-10-09) 47,313 GO Terms; optional_attrs(relations
hip)
107 GO IDs READ: 502S0.tab
15 GO IDs READ: 805S0.tab
6 GO IDs READ: 806S0.tab
5 GO IDs READ: 808S0.tab
247 GO IDs READ: 810S0.tab
HMS:0:00:00.318155 15,333 annotations READ: ../blah.gaf
GoSubDag: 363 sources in 715 GOs rcnt(True). 0 alt GO IDs
GoSubDag: namedtuple fields: NS level depth reldepth GO alt GO_name dcnt D1 tcnt tfreq tinfo childcnt REL REL_short rel id
GoSubDag: relationships: {'negatively_regulates', 'positively_regulates', 'part_of', 'regulates'}
Traceback (most recent call last):
File "/usr/local/bin/compare_gos.py", line 17, in
run()
File "/usr/local/bin/compare_gos.py", line 12, in run
obj = CompareGOsCli()
File "/usr/local/lib/python3.6/dist-packages/goatools/cli/compare_gos.py", line 77, in init
self.objgrpd = _ini.get_grouped(self.go_ntsets, self.go_all, self.gosubdag,
**self.kws)
File "/usr/local/lib/python3.6/dist-packages/goatools/cli/compare_gos.py", line 217, in get_grouped
kws_grpd['go2nt'] = self._init_go2ntpresent(go_ntsets, go_all, gosubdag)
File "/usr/local/lib/python3.6/dist-packages/goatools/cli/compare_gos.py", line 224, in _init_go2ntpresent
ntobj = namedtuple('NtPresent', " ".join(nt.hdr for nt in go_ntsets))
File "/usr/lib/python3.6/collections/init.py", line 401, in namedtuple
'identifiers: %r' % name)
ValueError: Type names and field names must be valid identifiers: '502S0'

[marade]

I figured out it's a typing issue. This works:

compare_gos.py --gaf=../blah.gaf -o compare.tab X502S0.tab X805S0.tab X806S0.tab X808S0.tab X810S0.tab

[dvklopfenstein]

Thanks for your interest in GOATOOLS and taking your time to write us.

That is great that compare_gos.py is working for you.

Can we close this issue?

[marade]

The problem isn't solved. It seems the least you could do is document this issue so that others do not experience the problem, but fixing it would be better.

[dvklopfenstein]

Seems like it will be an easy fix. Thank you for bringing this to our attention.

[marade]

Yes, I agree. I appreciate your work on this.

[dvklopfenstein]

The filename is no longer used as a field in a namedtuple, so now the compare GO terms script can support filenames of any format.

@tanghaibao , can you create a new release and upload to PyPI so that @marade and others may have access to the changes?

[tanghaibao]

@dvklopfenstein

Updated to v1.0.14.

[dvklopfenstein]

@marade , The changes are in. Please upgrade your GOATOOLS and give it a try. Please let us know how it works for you.

Thank you so much for taking your time to report this issue.

[marade]

Thanks for this. I think you can close the issue now.

[dvklopfenstein]

Okay. Terrific. Thank you for identifying and reporting this issue. We appreciate you taking your time to do that. And thank you for your interest in GOATOOLS.

Closing the issue...