gap4: command-line export of consensus seq?

  • douda

    douda - 2010-06-23

    Is there a way to export the consensus sequence from an assembly using gap4 from the command-line?

    This is simple enough from the GUI (save consensus as fasta, given a default quality threshold), but I have hundreds of project files to process and being able to do this from the command-line would be a massive help.

    Thank you.

  • James Bonfield

    James Bonfield - 2010-06-24

    There are some rather old Gap4 scripts at (or you can get there via Tracker -> Gap4 Scripts). This includes one to export consensus sequence and/or quality. I've no idea if it still works, but hopefully so as not much in Gap4 has changed since I wrote that.


  • douda

    douda - 2010-06-24

    Thanks. I've given it a try, with <databasename> as "AN1f2s1c3.0" and contig_number as "1":

    douda$ get_cons AN1f2s1c3.0 1

    but though I have no trouble exporting the consensus from this contig from the GUI, I get the following error message:

    Opening database AN1f2s1c3.0
    Thu 24 Jun 20:55:39 2010 Program terminated unexpectedly with signal 11.
    Thu 24 Jun 20:55:39 2010 This is probably a bug.
    Thu 24 Jun 20:55:39 2010 Please report all bug reports at
    Abort trap


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