[Biopython-dev] [Bug 1942] GenBank RecordParser fails on blank lines in features

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Feb 10 08:52:09 EST 2006


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED

------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2006-02-10 08:52 -------
I have checked in a fix for blank lines in Genbank feature entries.  The parser
will print a warning to screen and ignore the blank line(s).

See Bio/GenBank/__init__.py revision: 1.58

If you manage to find anymore "unusual Genbank files" please file another bug.

Thanks Leighton.



Leighton wrote:
> Is it possible that that run of spaces is stripped
> out by my ftp client during transfer?

I don't know - but if so, the same thing happened with my browser's FTP
support.  Even if this is just a file transfer issue, I still think we should
cope.  My personal opionion is this is just a one-off bad entry in the NCBI's
records, but that BioPython should be able to read anything they produce.

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