How to find the matching data b/w 2 files in perl?

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05-06-2010

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How to find the matching data b/w 2 files in perl?

Hi friends,,

i have find the matching data between 2files.
My file1 have a data like

Code:

rs3001336
rs3984736
rs2840532

File2 have a data like

Code:

rs3736330	  1	 2359237	A	G	0.28	   	1.099	        0.010
rs2840532	  1	 2359977	G	A	0.363 	0.3373	1.123	
rs3001336	  1	 2365193	G	A	0.0812	0.07319	1.12	
rs1129333	  1	 2367838	A	G	0.0817	0.0731	1.126	
rs3984736	  1	 2371236	G	A	0.0975	0.08456	1.133	
rs4531246	  1	 2394182	A	C	0.315	        0.9488	0.1

I have to find the matching data from file1 into the file2..
The output format should be like

Code:

rs3001336	  1	 2365193	G	A	0.0812	0.07319	1.12
rs2840532	  1	 2359977	G	A	0.363 	0.3373	1.123	
rs3984736	  1	 2371236	G	A	0.0975	0.08456	1.133

i need a program (in perl or R) to do this task.. pls friends help me

Thanks
Suresh

Last edited by pludi; 05-06-2010 at 03:19 AM.. Reason: code tags, please...

sureshraj

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Code:

for i in `cat file1 | sort | uniq`;do grep -w $i file2; done

---------- Post updated at 12:06 PM ---------- Previous update was at 11:42 AM ----------

how it is not working. can you please post your message here.. instead of private message.. so that some one help you....

Code:

kamaraj@kamaraj-laptop:~/Desktop/testing$ for i in `cat file1 | sort | uniq`;do grep -w $i file2; done
rs2840532	  1	 2359977	G	A	0.363 	0.3373	1.123	
rs3001336	  1	 2365193	G	A	0.0812	0.07319	1.12	
rs3984736	  1	 2371236	G	A	0.0975	0.08456	1.133	
kamaraj@kamaraj-laptop:~/Desktop/testing$ cat file1
rs3001336
rs3984736
rs2840532
kamaraj@kamaraj-laptop:~/Desktop/testing$ cat file2
rs3736330	  1	 2359237	A	G	0.28	   	1.099	        0.010
rs2840532	  1	 2359977	G	A	0.363 	0.3373	1.123	
rs3001336	  1	 2365193	G	A	0.0812	0.07319	1.12	
rs1129333	  1	 2367838	A	G	0.0817	0.0731	1.126	
rs3984736	  1	 2371236	G	A	0.0975	0.08456	1.133	
rs4531246	  1	 2394182	A	C	0.315	        0.9488	0.1
kamaraj@kamaraj-laptop:~/Desktop/testing$

itkamaraj

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One way to do it with Perl -

Code:

$
$
$ cat file1
rs3001336
rs3984736
rs2840532
$
$ cat file2
rs3736330         1      2359237        A       G       0.28            1.099           0.010
rs2840532         1      2359977        G       A       0.363   0.3373  1.123
rs3001336         1      2365193        G       A       0.0812  0.07319 1.12
rs1129333         1      2367838        A       G       0.0817  0.0731  1.126
rs3984736         1      2371236        G       A       0.0975  0.08456 1.133
rs4531246         1      2394182        A       C       0.315           0.9488  0.1
$
$ perl -lane '$ARGV eq "file1" ? $x{$_}=1 : defined $x{$F[0]} ? print : ""' file1 file2
rs2840532         1      2359977        G       A       0.363   0.3373  1.123
rs3001336         1      2365193        G       A       0.0812  0.07319 1.12
rs3984736         1      2371236        G       A       0.0975  0.08456 1.133
$
$

tyler_durden

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"Easy to read Perl"

Code:

#!/usr/bin/perl

use strict;
use warnings;

my $file1='file1' ;
my $file2='file2' ;
my @temparr=();
my @mainarr=();

open(FIL1, $file1) or die "Error: $!\n" ;

   my @arr1 = <FIL1> ;

close(FIL1) ;

open(FIL2, $file2) or die "Error: $!\n";

   my @arr2 = <FIL2> ;

close(FIL2) ;

  foreach my $record (@arr1) {
  chomp $record ;
  @temparr = grep(/$record/,@arr2) ;
  push(@mainarr, @temparr) ;
  }

print @mainarr ;

Code:

$ perl checkmatch.pl | sort
rs2840532	  1	 2359977	G	A	0.363 	0.3373	1.123	
rs3001336	  1	 2365193	G	A	0.0812	0.07319	1.12	
rs3984736	  1	 2371236	G	A	0.0975	0.08456	1.133	
$

pseudocoder

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Hi,

Looks like GWAS data
do you use PLINK? it has an option to do this

or you can do it using awk

Code:

awk 'FNR==NR {a[$1]++;next} $1 in a' file1 file2

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