[Biopython-dev] [Bug 2229] GenBank Scanner fails to scan over headers

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2229


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

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-03-12 12:05 EST -------
Link to download the file, about 28 MB

ftp://ftp.ncbi.nih.gov/genbank/gbvrl1.seq.gz

This starts:
------------------------------------------------
GBVRL1.SEQ           Genetic Sequence Data Bank
                          February 15 2007

                NCBI-GenBank Flat File Release 158.0

                          Viral Sequences (Part 1)

   72061 loci,    66147687 bases, from    72061 reported sequences


LOCUS       AB000048                2007 bp    DNA     linear   VRL 05-FEB-1999
DEFINITION  Feline panleukopenia virus DNA for nonstructural protein 1,
            complete cds.
ACCESSION   AB000048
...
------------------------------------------------


Much smaller test case, 81 KB compressed:

ftp://ftp.ncbi.nih.gov/genbank/gbuna.seq.gz

File starts:
------------------------------------------------
GBUNA.SEQ            Genetic Sequence Data Bank
                          February 15 2007

                NCBI-GenBank Flat File Release 158.0

                       Unannotated Sequences         

     211 loci,      114018 bases, from      211 reported sequences


LOCUS       AB086827                 901 bp    mRNA    linea
...
------------------------------------------------

In both cases, and I assume all these archives, there is a fairly uniform
header present, followed by the GenBank records.

I suppose we could/should spot these and skip them... does anyone know off hand
in EMBL does anything similar?


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