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peReadsFragmentMid.pl
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peReadsFragmentMid.pl
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#!/bin/usr/perl -w
use strict;
use 5.010;
use Getopt::Long;
my ($inFile,$fragment,%hash);
GetOptions(
'i|bam=s' => \$inFile,
'f|size=s' => \$fragment,
'h|help' => sub{usage()}
) || usage();
open IN,"samtools view $inFile|" or die "Can't open file $inFile:$!";
my($min_length,$max_length)=split /,/,$fragment;
while(<IN>){
chomp;
my @fields=split;
my($readName,$chrom,$pos,$Mchrom,$Mpos,$inSize,$seq)=@fields[0,2,3,6,7,8,9];
next if($Mchrom ne "=" || (abs $inSize)<$min_length || (abs $inSize)>$max_length);
my $readLen=length $seq;
if(exists $hash{$readName}){
next;
}else{
my $start;
$inSize=abs($inSize);
if($readLen<$inSize){
$pos>$Mpos?$start=$Mpos:$start=$pos;
}else{
$pos>$Mpos?$start=$pos:$start=$Mpos;
}
say join "\t",$chrom,$start+int($inSize/2)-1,$start+int($inSize/2),$inSize;
$hash{$readName}='';
}
}
sub usage{
print <<HELP;
Usage:perl $0 -i file.bam -f min_size,max_size >out.bed
Author:Yumei Li,2016-3-2
Revised by Yumei Li,2016-5-9,add comparison between read length and fragment range.
Revised by Yumei Li,2017-10-17, add auto detection of read length.
Description:This script prints fragment midpoints(The second point if the length is even) from input bam file based on size range [min_size,max_size].The fourth column of the output file is the fragment size.
Options:
-i|--bam FILE The input bam format file.(Pair-end reads)
-f|--size STRING The range of fragment length that seperated by comma.
-h|--help Print this help information.
HELP
exit(-1);
}