File: faformat.pl

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#!/usr/bin/perl

#Copyright (C) 2006-2008 Keio University
#(Kris Popendorf) <comp@bio.keio.ac.jp> (2006)
#
#This file is part of Murasaki.
#
#Murasaki is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#Murasaki is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with Murasaki.  If not, see <http://www.gnu.org/licenses/>.

###############
## formats sequences to pretty Fasta -- krisp
###############


use Getopt::Long;
use Pod::Usage;
use File::Basename;

BEGIN {
  unshift(@INC,(fileparse($0))[1].'perlmodules');
}

use Murasaki;

my $geneparse=getProg("geneparse");
die "Couldn't find useable geneparse program" unless $geneparse;

our ($name,$width)=(undef,75);
GetOptions('help|?' => \$help, man => \$man,
	   "title|name=s" => \$name, "width=i" => \$width,
	  );
pod2usage(1) if $help;
pod2usage(-exitstatus => 0, -verbose => 4) if $man;

($filename,$outfile)=@ARGV;

if($filename and -e $filename){
  open(INF,'-|',"$geneparse -c $filename") or die "Couldn't load geneparse.pl";
  my ($basename,$path,$suffix) = fileparse($filename);
  $name=$basename unless $name;
} else {
  print STDERR "File $filename not found. Waiting for input from stdin.\n" unless !$filename or $filename eq "-";
  open(INF,"-");
  $name="stdin" unless $name;
}
if($outfile){
  open(OUTF,">$outfile");
} else {
  open(OUTF,">-");
}


print OUTF ">$name\n";
do{
  $rbytes=read(INF,$_,$width);
  goto DONE unless $rbytes;
  s/\s//gmi; #kill all whitespace
  print OUTF $_."\n";
}until(!$rbytes);
DONE:

__END__

=head1 NAME

faformat.pl -- Reformat a sequence into fasta format

=head1 SYNOPSIS

faformat.pl [options] [<file-in> [<file-out>]]

=head1 OPTIONS

=over 8

=item B<--name|--title>
Sets the name to be provided on the first line of the fasta file.

=item B<--width=<columns>>
Column width to line wrap at (default 75).

=back

=head1 DESCRIPTION

Reads in a sequence, and puts it out in FastA format.

=cut