perl script: extracting mir-target information based on a list

Question

[biolab]

Dear all,

I have a file with mir-target information as well as a list file shown below. I wrote a script to extract mir-target information according to list file.

mir-target infor file:

miR156 AT1G19920.1:1068 5' AUGUUC-CUCUUGA-UGUUA 3'     ||o|| ||||o   |||o| 3' CACGAGUGAGAGAAGACAGU 5'
miR390 AT1G19920.1:1247 5' GGUCGUGAUCCUGCAGGAAUGGGCCA 3'    || ||o ||||o       ||o||   3' CC-GCGAUAGGGAGG----ACUCGAA 5'
miR172 AT1G19940.1:899 5' GGGCAGCUUCAU---GGUUGU 3'      ||||| ||||   |o|| | 3' UACGUCGUAGUAGUUCUAAGA 5'

list file:

miR156 AT1G19920.1:1068
miR172 AT1G19940.1:899

my perl script:

#!/usr/bin/perl -w
use strict;
if (@ARGV<1){print "perl sta.pl LIST INPUT"; exit;}

my %h;
open LIST, '<', $ARGV[0];
while(my $line = <LIST>){
    chomp $line;
    $h{$line} = 1;
}
close LIST;

open FH, '<', $ARGV[1];
while (my $line2 = <FH>){
    chomp $line2;
    my @a = split/\t/, $line2;
    my $mirsite = "$a[0]"."\t"."$a[1]";
     if (exists $h{$mirsite} ){
            print "$line2\n";
     }
}
close FH;

My PROBLEM is when running perl extr.pl list input I only got the miR172 line, the miR156 line can't be outputted.

Your help on my script will be much appreciated! THANKS!!

Answer 1

[Prakki Rama]

Assuming tab space, is between

miR156 AT1G19920.1:1068 \t 5' AUGUUC-CUCUUGA-UGUUA 3'     ||o|| ||||o   |||o| 3' CACGAGUGAGAGAAGACAGU 5'
________________________^^

Try this:

#!/usr/bin/perl -w
use strict;
if (@ARGV<1){print "perl sta.pl LIST INPUT"; exit;}
my %h;
open LIST, '<', $ARGV[0];
while(my $line = <LIST>){
    chomp $line;
    $h{$line} = 1;
}
close LIST;

open FH, '<', $ARGV[1];
while (my $line2 = <FH>){
    chomp $line2;
    my @a = split/\t/, $line2;
    my $mirsite = "$a[0]";#."\t"."$a[1]"; #Note this line
    #print "$mirsite\n";
     if (exists $h{$mirsite} ){
            print "$line2\n";
     }
}
close FH;

[biolab]

Hi Prakki, thanks a lot. Adding a "#" didn't work. I am sure my list file and input file are tab separated. Something is weird. Thanks anyway.

[biolab]

I finally sorted out the problem. When deleting all \r in the list and input files, the script works well.

Sorry for my non-biology-relavant post, but I do hope it could give little help to others.

[Prakki Rama]

but the above script with # worked for me! anyway good that, you could sort it out.:)

Answer 2

[Kenosis]

Here's another option that uses Perl to handle the file i/o (no need to explicitly open and close files), and a capture to grab the first part of your mir-target infor file lines:

use strict;
use warnings;

@ARGV == 2 or die 'perl sta.pl LIST INPUT';

my %h;

while (<>) {
    chomp;
    $h{$_} = undef;
    last if eof;
}

while (<>) {
    print if /(.+?)\s+\d+'/ and exists $h{$1};
}

Hope this helps!

[biolab]

Thank you Kenosis, I really appreciate your answer.