#236 Invalid genbank export: no space after feature name

closed-fixed
Gbrowse (196)
5
2008-01-16
2007-12-05
richard
No

"Download genbank format file" produces invalid genbank whenever a feature name is over 15 characters in length. In this case the feature interval is appended directly to the feature name with no space in between. The file then cannot be imported in to other software.

http://flybase.net contains many feature names which are over 15 characters so practically anything exported from Gbrowse on their website is invalid.

See line 26 of the example file invalid.gb

Discussion

  • richard

    richard - 2007-12-05

    An invalid genbank file produced by GBrowse (see line 26)

     
  • Scott Cain

    Scott Cain - 2008-01-16
    • status: open --> closed-fixed
     
  • Scott Cain

    Scott Cain - 2008-01-16

    Logged In: YES
    user_id=616711
    Originator: NO

    This is actually a BioPerl bug in Bio::SeqIO::genbank. I sent a suggested patch to the bioperl mailing list and attached it to this bug report. I did not restrict the feature type name to 15 char as I think that would result in a loss of information, but just adding a space between the name and the location will probably fix the format for most applications. If not, I think the decision for what to do should be left up to the individual user anyway.

    Scott

    File Added: genbank.pm.patch

     
  • Scott Cain

    Scott Cain - 2008-01-16
     

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