[Biopython-dev] [Bug 1903] New: GenBank parses fails with unusual quoting and line breaks

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1903

           Summary: GenBank parses fails with unusual quoting and line
                    breaks
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


I've been testing my new parser (recently checked in) and have discovered an
oddity that it currently fails on, locus Bd2676 in this file:

LOCUS       NC_005363            3782950 bp    DNA     circular BCT 22-NOV-2004
DEFINITION  Bdellovibrio bacteriovorus HD100, complete genome.
ACCESSION   NC_005363
VERSION     NC_005363.1  GI:42521650
KEYWORDS    complete genome.
SOURCE      Bdellovibrio bacteriovorus HD100
  ORGANISM  Bdellovibrio bacteriovorus HD100

Look at this bit, /note="\n                     hypothetical protein"

Normally this would be written as /note="hypothetical protein"


     gene            2594436..2596394
                     /locus_tag="Bd2676"
                     /db_xref="GeneID:2736184"
     CDS             2594436..2596394
                     /locus_tag="Bd2676"
                     /note="
                     hypothetical protein"
                     /codon_start=1
                     /evidence=not_experimental
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_969474.1"
                     /db_xref="GI:42524094"
                     /db_xref="GeneID:2736184"
                     /translation="MKRAYYSNDISRFLVDAPSSILGLLSKAHDFTLEEQQKNAWVKQ
                     IEILQTSLQGIPGHVYFEYSIPRVGKRVDLIVISGNALFSIEFKVGSSQFDSYAADQA
                     MDYALDLKNFHEGSHQIDIFPVLVATEATHTEALPSRFDDGVWSLTRTNSQNLSTHLQ
                     ALKTNAKGPEIDLLKWDASGYKPTPTIVEAAKALYSGHQVEEISRSDAGATNLSITSA
                     ALKKIIDESISQKKKTICLVTGVPGAGKTLVGLDLATSWNNPVANQHAVLLSGNGPLV
                     EILQEALAKDEANRSKASSPVKLSAARAKAKSFIQNIHHFRDEGLRTDAPPPEKVVIF
                     DEAQRAWNKTQTTKFMKTKKGVADFDHSEPEYLIKLMDRHADWAVIICLVGGGQEINT
                     GEAGISEWLDAIHNKFPHWQVCLPSTTSSADIPNIEKFVQAFSSRHHVDKNLHLTASV
                     RSFRSERVSDFMSALLDKDIDKAKALYSEIKEKYPIKLTRSLEEAKLWLKEKSRGNER
                     YGILASSGAGRLKAHGLDVKSRIEPVNWFLNDKKDVRSSFFMEDVATEFHVQGLELDW
                     TCVAWDIDFILSLKKETKFRSFAGTKWNNIKSSTDQSYLKNKYRVLLTRARQGLVLFV
                     PKGDPHDGTRPPGDYEELFSYLQYILND"

Patch to follow, once I work out what exactly my code is doing wrong.

Also, I have an existing patch pending for Bio/GenBank/__init__.py attached to
bug 1762.  Should any patch for this new bug be against the current CVS file,
or against the version after applying the bug 1762 patch?




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