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gap4: command-line export of consensus seq?

douda
2010-06-23
2013-04-18
  • 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 https://sourceforge.net/tracker/?group_id=100316&atid=749480 (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.

    James

     
  • 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 https://sourceforge.net/projects/staden/
    Abort trap