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GFF module can write unreadable GFF3 sequences. #99
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I am using the script glimmergff_to_proteins.py but I am getting this error. Can you suggest me how to troubleshoot since you are familiar with the code. Traceback (most recent call last): |
Discovered that GFF module supports writing out sequences with IDs that don't parse correctly on reading. If you submit a record to GFF for writing which has an ID which includes a space (e.g.
gi|564292986| some protein
) then it fails to parse that upon trying to read the same file, because the code is looking for an integer there. Alternatively if the record ID contained numbers (gi|564292986| 324 5348
) then you could trick it into finding an incorrect sequence start/end value.Code to reproduce the problem:
IMO, it would be best if the GFF module stripped everything after a space in record IDs when writing.
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