Hi, I have asked this question before , but as Admin said If i want to change my question , I have to ask new question instead of asking by answering the previous one, Anyhow, my question is :
I want to read through 2 different tab-delimited files of sequence coordinates and find the same columns entries in both files and print it out , one file is ref and the other one contains the the columns that I want to find in the ref file : I want to keep col1 - col2 and col3 of file one (ref file) and col1 - col2 - col 3 of file2
file one (ref file) :
Col1 Col2 Col3 Col4 Col5 ColX
chr start end (rest columns)
file2 :
Col1 Col2 Col3 Col4 Col5 ColX
chr start end (rest columns)
I have written script but I got error when i print it out :
Use of uninitialized value $line2 in split at ./match3.pl line 19, <$fh2> line 2458.
Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value $values2[0] in concatenation (.) or string at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value in concatenation (.) or string at ./match3.pl line 22, <$fh2> line 2458.
Use of uninitialized value in concatenation (.) or string at ./match3.pl line 22, <$fh2> line 2458.
my script is :
#!/usr/bin/perl
use strict;
use warnings;
open my $fh1, '<', 'file1';
open my $fh2, '<', 'file2';
my$line1 ;
my$line2 ;
while (<$fh1>) {
chomp;
my @values1 = split( "\t", $line1 );
close $fh1;
while (<$fh2>) {
chomp;
my @values2 = split( "\t", $line2 );
close $fh2;
if ( $values1[0] eq $values2[0] and $values1[1] eq $values2[1] and $values1[2] eq $values2[2])
{
print "$values2[0] \t $values2[1] \t $values2[2] \t \n" ;}}}
Thanks In Advance,
•
written
by
Ar Es •
1 answer
You are using a non optimal way of reading files, since you are reading file2 a number of times equal to the number of lines on file1. what I usually do in these kind of cases (looking for identical columns in several files) is to load the information needed from the smaller file in hashes if memory is not an issue, since perl is optimized for that. this is what I would simply do:
open FILE1, 'file1';
open FILE2, 'file2';
while (<FILE1>) {
if (/^((\S+\t){3})/) {
$data1{$1} = "";
}
}
close FILE1;
while (<FILE2>) {
if (/^((\S+\t){3})/) {
if ( exists $data1{$1} ) {
print "$1 \n" ;
}
}
}
close FILE2;
You may modify the regex while reading file1 and file2 in order to store and print whatever you may want to print afterwards
•
written
by
Jorge Amigo
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Actually, admin said edit your original question. And he also said: please try to format your code properly (indent lines with 4 spaces) to make it readable. Normally admin would then delete this question as a duplicate, but admin can't be bothered right now.
Anyway: I suggest you stop struggling with Perl and just implement this nice awk solution - http://www.unix.com/shell-programming-scripting/150318-matching-columns-two-files.html - just use
$1$2$3instead of$5$6$7.Thanks for your help admin :) and sorry if I said something wrong
No problem. Admins get tired and grumpy sometimes :)
I would like to ask, how much basic programming skills can we expect to accept a question? This script contains at least 7 big mistakes (like even failing to create filehandles properly). So this question has to do a lot with learning perl programming but nothing with bioinformatics. I don't like the general tendency of simply dropping some crappy code here and then have others fix it for you. I understand that OP is simply a beginner in perl, and that might excuse a lot, but I really ask you to ask this question on stack exchange and see how it fares. Closing as off-topic.