[Biopython-dev] [Bug 3069] Support for EMBL-line files from IMGT

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3069


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

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|More robust feature parser  |Support for EMBL-line files
                   |for GenBank/EMBL records    |from IMGT




------- Comment #15 from biopython-bugzilla at maubp.freeserve.co.uk  2010-05-18 07:48 EST -------
Retitling bug as "Support for EMBL-line files from IMGT in Bio.SeqIO".

Here is a start at parsing IMGT files based on subclassing the INSDC
code with slightly more flexible feature handling:
http://github.com/peterjc/biopython/tree/seqio-imgt

I've been testing using http://imgt.cines.fr/download/LIGM-DB/imgt.dat.Z

There are some interesting cases like AB114296 with:
FT   TRANSMEMBRANE-REGION2163..2240

We can if necessary work around some of the bad locations strings (see the
above branch). Note that there are still other problems in the IMGT data
like mismatched lengths.

Uri - Could you explain what your code was trying to do with the record header
parsing? An example or two would be great. Thanks!


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