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#!/usr/bin/perl
################################################################
# copyright (c) 2014,2015 by William R. Pearson and The Rector &
# Visitors of the University of Virginia */
################################################################
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under this License is distributed on an "AS
# IS" BASIS, WITHOUT WRRANTIES OR CONDITIONS OF ANY KIND, either
# express or implied. See the License for the specific language
# governing permissions and limitations under the License.
################################################################
################################################################
# clustal2fasta.pl
################################################################
# clustal2fasta.pl takes a standard clustal format alignment file
# and produces the corresponding FASTA file.
#
################################################################
use warnings;
use strict;
use Pod::Usage;
use Getopt::Long;
my ($shelp, $help, $trim) = (0, 0);
GetOptions(
"h|?" => \$shelp,
"help" => \$help,
);
pod2usage(1) if $shelp;
pod2usage(exitstatus => 0, verbose => 2) if $help;
unless (-f STDIN || -p STDIN || @ARGV) {
pod2usage(1);
}
my @seq_ids = ();
my %msa = ();
# read the first line, first should not be blank
my $title = <>;
while (my $line = <>) {
chomp $line;
next unless ($line);
next if ($line =~ m/^[\s:\*\+\.]+$/); # skip conservation line
my ($seq_id, $align) = split(/\s+/,$line);
if (defined($msa{$seq_id})) {
$msa{$seq_id} .= $align;
}
else {
$msa{$seq_id} = $align;
push @seq_ids, $seq_id;
}
}
for my $seq_id ( @seq_ids ) {
my $fmt_seq = $msa{$seq_id};
$fmt_seq =~ s/(.{0,60})/$1\n/g;
print ">$seq_id\n$fmt_seq";
}
__END__
=pod
=head1 NAME
clustal2fasta.pl
=head1 SYNOPSIS
clustal2fasta.pl clustal.msa
=head1 OPTIONS
-h short help
--help include description
=head1 DESCRIPTION
C<clustal2fasta.pl> takes a Clustal format interleaved multiple
sequence alignment and produces the corresponding fasta format library.
=head1 AUTHOR
William R. Pearson, wrp@virginia.edu
=cut
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