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Revision 1.3 - (download) (as text) (annotate)
Mon Jan 4 20:14:57 2010 UTC (9 years, 10 months 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, 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_2010_0118, 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
Changes since 1.2: +4 -4 lines
Switched to ANNO server

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

use ANNOserver;

# Parms are FASTA input file name, genus, species.
# Produce geneID, type, contig, begin, strand, len on STDOUT.

my $annoObject = ANNOserver->new();
my ($file, $genus, $species) = @ARGV;

open FASTAIN, "<$file";
my $geneCalls = $annoObject->call_genes(\*FASTAIN);
# We throw away the FASTA string returned by call_genes.
my (undef, $geneList) = @$geneCalls;
for my $geneData (@$geneList) {
    my ($gene, $contig, $begin, $strand, $len) = @$geneData;
    print join("\t", $gene, 'peg', $contig, $begin, $strand, $len);
}
close FASTAIN;
open FASTAIN, "<$file";
my $rnaCalls = $annoObject->find_rnas(\*FASTAIN, $genus, $species, 'Bacteria');
# We throw away the FASTA string returned by find_rnas.
my (undef, $rnaList) = @$rnaCalls;
for my $rnaData (@$rnaList) {
    my ($rna, $contig, $begin, $strand, $len) = @$rnaData;
    print join("\t", $rna, 'rna', $contig, $begin, $strand, $len);
}

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