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Revision 1.4 - (download) (as text) (annotate)
Sun Jul 8 21:03:27 2018 UTC (16 months ago) by golsen
Branch: MAIN
CVS Tags: HEAD
Changes since 1.3: +7 -4 lines
Add support for mafft.

#! /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)
   -f    # Align with mafft
   -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/f//g ) { $prog = 'mafft' }
    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 'mafft'  ? scalar gjoalignment::align_with_mafft( \@seqs )
          : $prog eq 'muscle' ? scalar gjoalignment::align_with_muscle( \@seqs )
          :                     scalar gjoalignment::align_with_clustal( \@seqs );

gjoseqlib::write_fasta( $align );

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