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Revision 1.1 - (download) (as text) (annotate)
Mon Jan 19 21:49:02 2009 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, rast_rel_2009_02_05, 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_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, rast_rel_2009_03_26, mgrast_dev_10262011, HEAD
Tutorial examples.

#!/usr/bin/perl -w
use strict;

use ERDB;

my $erdb = ERDB::GetDatabase('Sprout');
my $genomeID = shift @ARGV;
my $qh = $erdb->Get('Genome HasContig Contig', "Genome(id) = ?", [$genomeID]);
while (my $contig = $qh->Fetch()) {
    my $contigID = $contig->PrimaryValue('Contig(id)');
    my $seq = &GetContigSeq($erdb, $contigID);
    my $len = length($seq);
    my $prefix = substr($seq, 0, 50);
    print "$contigID\t$len\t$prefix\n";
}

sub  GetContigSeq {
    my ($erdb, $contigID) = @_;
    my $retVal = join("", $erdb->GetFlat("Contig IsMadeUpOf Sequence", "Contig(id) = ? ORDER BY IsMadeUpOf(start-position)",
                                         [$contigID], "Sequence(sequence)"));
    return $retVal;
}

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