how to match a numers from file1 to file 2??Ps help me..

Shell Programming and Scripting
1

Hi firends,
I need to write a program in perl for following task,
I have a data like following numbers in file1.txt

1061338
1159781
1161717
1920355
1924487
2996733
3121872
3124510

I have to search the matching numbers in file2,my file2 is have a multiple columns like this

rs3934834	  1	   1045729	   A	G	0.1791	0.2054	0.8441	
rs3737728	  1	   1061338	   A	G	0.2845	0.2809	1.018	
rs6687776	  1	   1070488	   A	G	0.1768	0.1956	0.8833
rs9651273	  1	   1071463	   A	G	0.2743	0.2689	1.028	
rs4970405	  1	   1088878	   G	A	0.0922	0.0757	1.24	
rs1272625	  1	   1089873   G	A	0.1369	0.1231	1.13	
rs2298217	  1	   1104902   A	G	0.1448	0.1542	0.9286	
rs4970362	  1	   1134661	   A	G	0.3793	0.3954	0.9346

the underlined column have to matched with file1..But i dont know how to write a program for this task..I need out put like file2 for matching numbers only...Pls any one help me & give me a program in perl..
my output should be like

rs6596796	6	120522	A	G	0.1058	0.09469	
rs1535053	6	126089	G	A	0.2155	0.2151	
rs12192106	6	137664	A	G	0.06956	0.07949	
rs6913464	6	139090	A	G	0.1702	0.1663	
rs9405480	6	144199	A	G	0.1869	0.1771	
rs9392299	6	148909	G	A	0.07122	0.06203	
rs1418708	6	150610	A	G	0.1386	0.1374
rs1418707	6	150800	G	A	0.192	       0.1631
2

I didn't understand the following statement in your question.
The third column of file2 have a matching numbers of file 2.

my understanding is , Need to match the 3rd column of file2 with file1 content. You need a output from file2 matched lines with file1.

Give me your desired output.

3

Hi Nila thanks for reply,

simply say i have match the file1 & file 2.the file2 have data like as i said before..the third column of file2 have a matching numbers with file1.which means

rs6596796	6	120522	A	G	0.1058	0.09469	1.132	
rs1535053	6	126089	G	A	0.2155	0.2151	1.003	
rs12192106	6	137664	A	G	0.06956	0.07949	0.86	
rs6913464	6	139090	A	G	0.1702	0.1663	1.028	
rs9405480	6	144199	A	G	0.1869	0.1771	1.068	
rs9392299	6	148909	G	A	0.07122	0.06203	1.16	
rs1418708	6	150610	A	G	0.1386	0.1374	1.01	
rs1418707	6	150800	G	A	0.192	0.1631	1.219

the under lined numbers r have to match with file1...and my output should be like this..

rs6596796	6	120522	A	G	0.1058	0.09469	1.132	
rs1535053	6	126089	G	A	0.2155	0.2151	1.003	
rs12192106	6	137664	A	G	0.06956	0.07949	0.8657	
rs6913464	6	139090	A	G	0.1702	0.1663	1.028	
rs9405480	6	144199	A	G	0.1869	0.1771	1.068	
rs9392299	6	148909	G	A	0.07122	0.06203	1.16	
rs1418708	6	150610	A	G	0.1386	0.1374	1.01	
rs1418707	6	150800	G	A	0.192	        0.1631	1.219	3.

pls help me nila..this is very urgent..write a program for this task

4

From the data it looks like the data issorted.
The file1 is sorted.
And file2 is sorted on column 3.
Is this correct?
Then I would consider Unix "paste" is the best command.

5

[root]# perl -lane "BEGIN { open(FH,'file1');@con=<FH>;}print if grep(/@F[2]/,@con)" file2
rs3737728 1 1061338 A G 0.2845 0.2809 1.018

Thanks,
Penchal

---------- Post updated at 12:39 AM ---------- Previous update was at 12:35 AM ----------

Hi ,

if third coulmn of file2 matches with file1 in above case ,

output must be

rs3737728 1 1061338 A G 0.2845 0.2809 1.018

Am i right

Thanks,
Penchal

6

If it is not sorted then try this:

while read xx ; do
 egrep " $xx " file2
done < file1

Not the best. Draw backs:

  1. If you have 10,000 records in file1 then you will be calling egrep so many times.
  2. This code is not looking for the value exclusively in column 3, but in the whole record. That is, if column 1 has the same value then you are .......
7

Try this,

use strict;
use warnings;
use Data::Dumper;


open FH1,"file" or die "Can't open the file $!";
open FH2,"file1" or die "Can't open the file $!";
open OUTPUT,"+>output_file" or die "Can't open the file $!";

while (<FH1>)
{
        my $line=$_;

        while (<FH2>)
        {
                my ($a,$b,$c)=split(' ');
                if($c == $line)
                {
                        print OUTPUT $_ ;
                }

        }
}