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vloux / ProteoRE

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JVenn Bug : proteore.org #315

Open yvandenb opened 3 years ago

yvandenb commented 3 years ago

History: http://www.proteore.org/u/yvdb/h/ovariancortex Version tool used: Venn diagram [JVenn] (Galaxy Version 2021.05.12) Same bug observed using Venn diagram [JVenn] (Galaxy Version 2020.01.10) NB: each list contains > 6500 entries

Traceback (most recent call last): File "/home/proteore/shed_tools/toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/e744a43171ff/proteore_venn_diagram/venn_diagram.py", line 187, in process( args ) File "/home/proteore/shed_tools/toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/e744a43171ff/proteore_venn_diagram/venn_diagram.py", line 171, in process write_summary(args.summary, args.input) File "/home/proteore/shed_tools/toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/e744a43171ff/proteore_venn_diagram/venn_diagram.py", line 149, in write_summary a, b = input_to_dict(inputs) File "/home/proteore/shed_tools/toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/e744a43171ff/proteore_venn_diagram/venn_diagram.py", line 57, in input_to_dict file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # gets ids from defined column IndexError: list index out of range

vloux commented 3 years ago

Reproducible. Empty lines in input files are not filtered and make Jvenn fail.

Should the tool fltered it without launching an error or should the error be explicit ?

yvandenb commented 3 years ago

Should the tool fltered it without launching an error I would vote for this solution

yvandenb commented 3 years ago

Not a bug in itself, rather an improvement => carriage return or linefeed in the list of entries should normally be removed...