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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;
$Getopt::Std::STANDARD_HELP_VERSION=true;
getopts('DCncBrl');
if($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\" - $outfile");
}
if($opt_r or $inseq=~m/^[10]+$/){
%bases=("00" => "A", "01" => "C", "10" => "G", "11" => "T");
while($inseq=~m/([10]{2})/g){
# print "Parsing $` - $& - $'\n";
$outseq.=$bases{$1};
}
$outseq=lc($outseq) if $opt_l;
print OUTF "$outseq";
}else{
$inseq=~s/[ \.a-]/00/gi;
$inseq=~s/c/01/gi;
$inseq=~s/[gu]/10/gi;
$inseq=~s/[t]/11/gi;
$inseq=~s/[^01]//g unless $opt_n;
print OUTF "Binary: " unless $opt_c;
print OUTF "$inseq";
unless($opt_D){
print "\n" unless $opt_B;
$inseq=bin2dec($inseq);
print OUTF "Decimal: " unless $opt_c;
print OUTF "$inseq";
}
}
close(OUTF);
print "\n";
sub main::HELP_MESSAGE {
print <<ENDTEXT
Usage: $0 [-c] [-d] [-n] [<in file>] [<out file>]
If you don't specify an infile or outfile, stdin/stdout is used.
-C specifies pretty formatted output (can't imagine why...but ok)
-c specifies clean output. (ie: no labels)
-D skip decimal output
-B skip binary output
-n don't erase non-nucleotides (default is set blasters to kill)
-r reverse (binary to bases)
-l output lowercase
ENDTEXT
;
}
sub main::VERSION_MESSAGE {
}
sub bin2dec {
my $arg=shift;
my ($pos,$ret)=(0,0);
foreach (split(//,reverse($arg))){
$ret+=$_<<$pos;
$pos++;
}
return $ret;
}
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