[Biopython-dev] [Bug 2520] New: Reading ACE assembly contig files in Bio.SeqIO

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Jun 17 11:23:59 UTC 2008


           Summary: Reading ACE assembly contig files in Bio.SeqIO
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk

As I suggested on the mailing list, we could use Bio.Sequencing.Ace to parse
ACE assembly files, and then turn each contig into a SeqRecord using the
consensus sequence.

I will attach a basic implementation which only uses the consensus sequence and
its name.  For now this ignores all the meta data and in particular the read

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