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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/>.
use Getopt::Std;
use File::Basename;
BEGIN {
unshift(@INC,(fileparse($0))[1].'perlmodules');
}
use Murasaki;
$Getopt::Std::STANDARD_HELP_VERSION=true;
getopts('chRC');
if($opt_h){HELP_MESSAGE();exit(0);}
($filename,$outfile)=@ARGV;
if($filename and -e $filename){
$inseq=`$root/geneparse.pl -c $filename`;
my ($basename,$path,$suffix) = fileparse($filename);
$name="$basename-revcomp";
} else {
print STDERR "File $filename not found. Waiting for input from stdin.\n" unless !$filename or $filename eq "-";
while($_=<STDIN>){
chomp;
$inseq.=$_;
}
$name="stdin";
}
$outfile="-" unless $outfile;
if($opt_c){
open(OUTF,">$outfile");
}else{
open(OUTF,"|$root/faformat.pl --name=\"$name\" - $outfile");
}
$inseq=reverse($inseq) unless $opt_C;
$inseq=~y/agtcAGTC/tcagTCAG/ unless $opt_R;
print OUTF $inseq;
close(OUTF);
sub main::HELP_MESSAGE(){
print <<ENDTEXT
Usage: $0 [-c] [-R] [-C] [<in file> [<out file>] ]
If you don't specify an infile or outfile, stdin/stdout is used.
-c specifies clean output (ie: just the sequence)
-R specifies reverse ONLY
-C specifies complement ONLY
Now if you're wondering what mixing -R and -C do...
ENDTEXT
;
}
sub main::VERSION_MESSAGE(){
}
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