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    BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1207 ] Errors in writing GenBank files
    Date:
    01/06/16 15:47
    Submitted by:
    B_Fristensky     		Assigned to:
    B_Fristensky
    Category:
    bioLegato     		Priority:
    5
    Ticket group:
    Bug     		Resolution:
    Resolved
    Summary:
    Errors in writing GenBank files
    Original submission:
    BioLegato adds extra junk when writing GenBank files. eg.

    1) Blank line between LOCUS and DEFINITION lines.
    LOCUS SEG_LSTISF 6396 bp DNA linear PLN 25-AUG-2010

    DEFINITION Lactuca sativa.
    ACCESSION AH005956
    VERSION AH005956.1 GI:2981179

    2) Superfluous ORIGIN line indented

    /note="region B; 3' flanking region of T-DNA insertion
    site"
    ORIGIN
    1
    ORIGIN
    1 aagcttgtga atctatttcc gcgcaatccc atgtctctgt tgcatcatct tgaagagctt

    To reproduce:

    bldna --> File --> View sequences --> GenBank --> Run
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    This did indeed turn out to be a bug in readseq. A note has been sent to Don Gilbert to fix the problem, which is in the most recent versions: 2.1.27 and 2.1.30.

    In the meantime, the simplest workaround is to deal with the problem only where it matters. Most programs don't care about these differences. Individual BioLegato menus will be fixed to deal with these few cases. It would be a lot of work to write a general script, because it would have to check both input and output formats before deciding whether to run readseq.     		01/13/16 20:16 B_Fristensky
    A test of READSEQ at the command line shows that this is actually a bug in READSEQ, not in BioLegato. 01/13/16 19:06 B_Fristensky
    This may actually be a bug in READSEQ, which is called
    by View sequences. The workaround would be to write a
    script that leaves the file alone if it's GenBank
    format, and filters it through READSEQ for other formats.     		01/06/16 16:03 B_Fristensky
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Open 01/13/16 20:16 B_Fristensky
    resolution_id Not Resolved 01/13/16 20:16 B_Fristensky
    close_date 12/31/69 19:00 01/13/16 20:16 B_Fristensky
    status_id Pending 01/06/16 15:47 B_Fristensky
    assigned_to unset 01/06/16 15:47 B_Fristensky
    resolution_id Unset 01/06/16 15:47 B_Fristensky

     
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