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Revision 1.1 - (download) (as text) (annotate)
Sat Feb 20 16:40:06 2010 UTC (10 years ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2010_0526, 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, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
get all protein sequences for complete prokaryotic genomes

use strict;
use SeedEnv;

my $sapO    = SAPserver->new;
my $genH    = $sapO->all_genomes(-complete => 1);
my @genomes = keys(%$genH);
my $prokH   = $sapO->is_prokaryotic( -ids => \@genomes);
foreach my $genome (grep { $prokH->{$_} } sort { $a <=> $b } @genomes)
{
    my $genH2 = $sapO->all_features( -ids => [$genome], -type => 'peg' );
    my $pegs  = $genH2->{$genome};
    my $funcH = $sapO->ids_to_functions( -ids => $pegs );
    my $seqH  = $sapO->ids_to_sequences( -ids => $pegs, -protein => 1 );
    foreach my $peg (sort { &SeedUtils::by_fig_id($a,$b) } @$pegs)
    {
	my $seq = $seqH->{$peg};
	if ($seq) 
	{
	    my $func = $funcH->{$peg} ? $funcH->{$peg} : '';
	    print ">$peg $func\n$seq\n";
	}
    }
}

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