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extract.correct.mate.pairs.pl
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#!/usr/bin/env perl
###############################################################################
#
# scriptname
#
# Short description
#
# Copyright (C) 2012 Mads Albertsen
#
# This program 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.
#
# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
#
###############################################################################
#pragmas
use strict;
use warnings;
#core Perl modules
use Getopt::Long;
#locally-written modules
BEGIN {
select(STDERR);
$| = 1;
select(STDOUT);
$| = 1;
}
# get input params
my $global_options = checkParams();
my $inputfile;
my $endlength;
$inputfile = &overrideDefault("inputfile.txt",'inputfile');
$endlength = &overrideDefault(3000,'endlength');
my %reads;
my %contigs;
my $progress = 0;
my $mpcount = 0;
######################################################################
# CODE HERE
######################################################################
open(IN, $inputfile) or die("Cannot read file: $inputfile\n");
open(OUT1, ">p1.fa") or die("Cannot create file: p1.fa\n");
open(OUT2, ">p2.fa") or die("Cannot create file: p2.fa\n");
while ( my $line = <IN> ) {
chomp $line;
my @splitline = split(/\t/, $line);
if ($line =~ m/\@SQ/) { #Get the lenfth of each scaffold and store it in an array
my @contigname = split(/:/, $splitline[1]);
my @contiglength = split(/:/, $splitline[2]);
$contigs{$contigname[1]} = $contiglength[1];
}
else {
if ($line !~ m/(\@PG|\@HD|\@SQ)/) { #If we are not in the header region
if ( ($contigs{$splitline[2]}-$splitline[3] - length($splitline[9]) < $endlength) or ($splitline[3] < $endlength) ){ #Check if the read map in one of the ends of the scaffolds
my @header = split(/_/,$splitline[0]);
if (exists($reads{$header[0]})){ #Check if the other pair of the read have been seen before
my @oldread = split(/\t/,$reads{$header[0]});
if ($oldread[1] ne $splitline[2]){ #Check if the two reads map to different scaffolds
my @readpair = split(/:/,$header[1]);
$mpcount++;
if ($readpair[0] == 1){ #Print the reads to the right file
print OUT1 ">$splitline[0]\n";
print OUT1 "$splitline[9]\n";
print OUT2 ">$oldread[0]\n";
print OUT2 "$oldread[2]\n";
}
else{
print OUT2 ">$splitline[0]\n";
print OUT2 "$splitline[9]\n";
print OUT1 ">$oldread[0]\n";
print OUT1 "$oldread[2]\n";
}
}
}
else{
$reads{$header[0]} = "$splitline[0]\t$splitline[2]\t$splitline[9]";
}
}
$progress++;
if ($progress == 1000000){
print "$progress reads processed\n";
$progress = 0;
}
}
}
}
print "$progress reads processed\n";
print "$mpcount mate-pairs extracted\n";
close IN;
close OUT1;
close OUT2;
######################################################################
# TEMPLATE SUBS
######################################################################
sub checkParams {
#-----
# Do any and all options checking here...
#
my @standard_options = ( "help|h+", "inputfile|i:s", "endlength|e:s");
my %options;
# Add any other command line options, and the code to handle them
#
GetOptions( \%options, @standard_options );
#if no arguments supplied print the usage and exit
#
exec("pod2usage $0") if (0 == (keys (%options) ));
# If the -help option is set, print the usage and exit
#
exec("pod2usage $0") if $options{'help'};
# Compulsosy items
#if(!exists $options{'infile'} ) { print "**ERROR: $0 : \n"; exec("pod2usage $0"); }
return \%options;
}
sub overrideDefault
{
#-----
# Set and override default values for parameters
#
my ($default_value, $option_name) = @_;
if(exists $global_options->{$option_name})
{
return $global_options->{$option_name};
}
return $default_value;
}
__DATA__
=head1 NAME
extract.correct.mate.pairs.pl
=head1 COPYRIGHT
copyright (C) 2012 Mads Albertsen
This program 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.
This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
=head1 DESCRIPTION
=head1 SYNOPSIS
extract.correct.mate.pairs.pl -i [-h -e]
[-help -h] Displays this basic usage information
[-inputfile -i] Inputfile.
[-endlength -e] Output reads X bp from the ends (default: 3000)
=cut