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.
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.
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/