Mercurial > repos > messersc > jamm
view readshifter.pl @ 1:243f75d0ed6e draft default tip
Uploaded.
Includes new release 1.0.7 with fixed optional controls.
author | messersc |
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date | Thu, 19 Feb 2015 05:39:45 -0500 |
parents | d42f4d78c85e |
children |
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######################################################################## # JAMMv1.0.7rev1 is a peak finder for joint analysis of NGS replicates. # Copyright (C) 2014-2015 Mahmoud Ibrahim # # 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/>. # # Contact: mahmoud.ibrahim@mdc-berlin.de ######################################################################## use feature qw(say); # ================== # Parsing Arguments # ================== #initialize to NULL my $bed_file = NULL; #bed file my $shift_size = NULL; #shift size my $read_length = NULL; #read length #Parse the arguments $bed_file = $ARGV[0]; #bed file $shift_size = $ARGV[1]; #shift size $read_length = $ARGV[2]; #read length #=======================> DONE! # ======================================== # Parse the bed file and extend the reads # ======================================== #open the file open(DATA, $bed_file) || die("Can't open the bed file, probably you gave me the wrong path!"); #loop through the rest of the file line by line (To do: look for a faster way) while (<DATA>) { my ($start, $strand) = split(/\t/,$_,2); $strand =~ s/\015?\012?$//; #plus strand if ($strand eq '+') { #do nothing } #minus strand elsif ($strand eq '-') { $start = $start - $shift_size + $read_length; #difference between $start and $end should be equal to fragment length ($shift_size) } #bad format else { die("It appears the bed file is not formatted properly. Specifically, I expect to find either + or - in the second column, but I found something else!"); } if ($start >= 0) { #Now write the new line say join "\t", $start, $strand; } } #=======================> DONE!