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Revision 1.4 - (download) (as text) (annotate)
Thu Nov 11 17:45:25 2010 UTC (9 years ago) by disz
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2011_0119, 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, mgrast_dev_04012011, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.3: +1 -1 lines
FigFam 6 digit problem

use strict;
use FIG;
my $fig = new FIG;

@ARGV == 1 or die "Usage: build_prok_nonff_fasta ff_dir\n";

my $figfams = shift;

-d $figfams or die "Invalid figfams dir $figfams\n";

if (!open(F, "<", "$figfams/families.2c"))
{
    die "could not find open $figfams/families.2c: $!";
}

my %FFpegs;

while (<F>)
{
    if (/^FIG\d+\t(fig\|\d+\.\d+\.peg\.\d+)/)
    {
	$FFpegs{$1} = 1;
    }
}

close(F);

foreach my $genome (grep { $fig->is_prokaryotic($_) } $fig->genomes('complete'))
{
    foreach my $ent (@{$fig->all_features_detailed_fast($genome)})
    {
	my($peg, undef, undef, $type, undef, undef, $func) = @$ent;
	#print STDERR "peg=$peg type=$type func=$func ffpeg=$FFpegs{$peg}\n";
	next if $type ne 'peg';
	next if $FFpegs{$peg};
	next if &FIG::hypo($func);

	my $seq = $fig->get_translation($peg);
	if ($seq)
	{
	    #print ">$peg $func\n$seq\n";
	    &FIG::display_id_and_seq("$peg $func", \$seq, \*STDOUT);
	}
    }
}


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