Mercurial > repos > messersc > jamm
view readshifter.pl @ 0:d42f4d78c85e draft
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author | messersc |
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date | Wed, 17 Dec 2014 10:40:23 -0500 |
parents | |
children | 243f75d0ed6e |
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#!/usr/bin/perl ############################################## #### Shifts minus strand reads by read length #### Perl script ############################################# 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!