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Revision 1.1 - (download) (as text) (annotate)
Mon Oct 1 17:32:07 2007 UTC (12 years, 4 months ago) by golsen
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
Function to get the ids or sequences of features that match a given role.
Uses FIG::seqs_with_role.

# -*- perl -*-
#
# Copyright (c) 2003-2007 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

use Carp;
use Data::Dumper;

use FIG;
my $fig = new FIG;

use strict;

my $usage = <<End_of_Usage;

Usage: features_with_role    [options] 'Role' > ids
       features_with_role -s [options] 'Role' > fasta_seqs

Options:

   -a          Include all sequences, not just those with a fid
   -g genome   Limit to genome
   -s          Output protein sequences
   -w whom     Include assignments by specified user

End_of_Usage

my $all;
my $genome;
my $seqs;
my $whom;

while ( $ARGV[0] =~ /^-/ )
{
    $_ = shift @ARGV;
    if    ( s/^-a// ) { $all    = 1 }
    elsif ( s/^-g// ) { $genome = $_ || shift @ARGV }
    elsif ( s/^-s// ) { $seqs   = 1 }
    elsif ( s/^-w// ) { $whom   = $_ || shift @ARGV }
    else
    {
        print STDERR "Bad flag '$_'.\n\n$usage\n";
        exit;
    }
}

my $role = shift @ARGV
    or print STDERR "Missing role\n$usage"
    and exit;

my @ids =  grep { $all || /^fig\|/ }
           $fig->seqs_with_role( $role, $whom, $genome );

if ( ! $seqs )
{
    print join( "\n", @ids ), "\n";
}
else
{
    my ( $fid, $seq );
    foreach $fid ( @ids )
    {
        my $seq = $fig->get_translation( $fid );
        $seq or next;
        $seq =~ s/(.{1,60})/$1\n/g;
        print ">$fid\n$seq";
    }
}

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