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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1189 ] extract does not preserve GenBank annotation
    Date:
    09/19/13 16:47
    Submitted by:
    B_Fristensky
    Assigned to:
    B_Fristensky
    Category:
    bioLegato
    Priority:
    5
    Ticket group:
    Bug
    Resolution:
    Unset
    Summary:
    extract does not preserve GenBank annotation
    Original submission:
    Description:
    1. In bldna, read in one or more GenBank entries using File --> Open.
    2. Edit --> Extract

    The new bldna window will have the sequences, but not the annotation. This is because extract uses gde format to save the data in a temporary file, which does not include the annotation. You can demonstrate that by saving GenBank entries in gde format.

    Proposed fix: The simple fix is to use GenBank format for extract only in bldna, since other bioLegatos don't need to deal with GenBank annotation. That is fine if all you care about is sequences. The problem is that comments are not correctly preserved when writing and reading GenBank format. When writing GenBank, bioLegato eliminates non-blank characters and adds blanks every 10 characters. When reading in, only legal nucleotides are read.


    Short term fix: change extract in bldna to use GenBank format. I have made this change in bldna and tested it,and it works. The only thing that doesn't work is the comment issue above.

    Longer term fix: Let's think about having BioLegato save the GenBank annotation in gde format.


    Platform: BioLegato 0.8.0, BIRCH 2.96

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    Ticket change history
    Field Old value Date By
    assigned_to unset 08/08/15 13:22 B_Fristensky

     

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