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Convert perl program to shell

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# 1  
Old 02-01-2012
Convert perl program to shell
Hi is there a way that i can convert this simple perl program into shell script
Code:
#!usr/bin/perl -w
use strict;
use warnings;

open INPUTFILE, "uniqprobecoordinates.out" || die "canot open the file $!";
open OUTPUTFILE, ">", "1_4reads.out";

while(<INPUTFILE>)
    {
        chomp;
        my $num = `samtools view  110611_s_4.hg18.filtered.sorted.bam $_ | wc -l`;
        print OUTPUTFILE "$_\t$num\n";
    }

close(INPUTFILE);
close(OUTPUTFILE);

Moderator's Comments:
Mod Comment How to use code tags when posting data and code samples.
Last edited by Franklin52; 02-01-2012 at 05:25 PM.. Reason: Please use code tags for data and code samples, thank you
# 2  
Old 02-01-2012
Maybe. What does it do? What input do you have, and what output do you want?
This User Gave Thanks to Corona688 For This Post:
bhargavpbk88
# 3  
Old 02-01-2012
this is a command in bash using samtools package
samtools view 110611_s_4.hg18.filtered.sorted.bam chr3:22937492-3299833 | wc -l

this gives me output like a number 8
i want output file like
chr3:22937492-3299833 8

And the input file has many rows having chromosome information for each chromosome i want output and corresponding number from command i mentioned in the top.
i tried in perl but its taking very long time as the files are very huge.

Thanks.
# 4  
Old 02-01-2012
Untested.
Code:
#! /bin/bash

while read x
do
    num=`samtools view  110611_s_4.hg18.filtered.sorted.bam $x | wc -l`
    echo -e "$x\t$num" >> 1_4reads.out
done < uniqprobecoordinates.out

But if the file is huge, it should be equally slow (or rather slower) in bash.
This User Gave Thanks to balajesuri For This Post:
bhargavpbk88
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