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Revision 1.1 - (download) (as text) (annotate)
Wed Nov 21 20:41:05 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
add code to fix frameshifts in a genome

use FS_RAST;

use FIGO;
my $figO = new FIGO;

($genome = shift @ARGV) || die "usage: find_poss_fs Genome";

my $genomeO = new GenomeO($figO,$genome);

foreach $pegO ($genomeO->features_of('peg'))
{
    if ($fs = $pegO->possible_frameshift)
    {
	print STDERR "trying to correct ",$pegO->id,"\n";
	my($contig,$beg,$end,$dna,$peg) = @$fs;
	my $pegO = new FeatureO($figO,$peg);
	my $params = {};
	$params->{family}  = [[$peg,"",$pegO->prot_seq]];
	my($loc,$translation,$genomes,$annotation) = &FS_RAST::best_match_in_family($params,[$contig,$beg,$end,$dna],);
	if ($loc)
	{
	    print join("\n//\n",($pegO->id,$loc,$translation,join(",",@$genomes),$annotation)),"///\n";
	}
	else
	{
	    print STDERR "did not fix\n";
	    print &Dumper([$contig,$beg,$end,$dna,$peg]);
	}
    }
}

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