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Revision 1.3 - (download) (as text) (annotate)
Tue Jan 19 01:57:39 2010 UTC (10 years, 2 months ago) by golsen
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
Changes since 1.2: +26 -108 lines
Add support for alignment with muscle.

#! /usr/bin/perl -w
#
# Copyright (c) 2003-2006 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.
#
#  Align sequeneces with clustalw or muscle and output in fasta.
#

use strict;
use gjoseqlib;
use gjoalignment;

my $usage = <<'End_of_Usage';
Align fasta format sequences

Usage: align_fasta  [options]   fasta-file > aligned
       align_fasta  [options] < fasta-file > aligned

Options:

   -c    # Align with clustalw (D)
   -m    # Align with muscle

End_of_Usage

my $prog = 'clustal';

while ( @ARGV && $ARGV[0] =~ s/^-// )
{
    local $_ = shift;
    if ( s/c//g ) { $prog = 'clustal' }
    if ( s/m//g ) { $prog = 'muscle' }
    if ( m/./   ) { print STDERR "Bad flag '$_'.\n\n", $usage; exit }
}

my @seqs = gjoseqlib::read_fasta( $ARGV[0] || \*STDIN );

@seqs or print STDERR "No input sequences.\n\n", $usage and exit;

my @align = @seqs < 2         ? @seqs
          : $prog eq 'muscle' ? gjoalignment::align_with_muscle( \@seqs )
          :                     gjoalignment::align_with_clustal( \@seqs );

gjoseqlib::print_alignment_as_fasta( @align );

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