Re: match two files

This will probably shorten the running time but I don't have your data to test it on, so good luck.

#!/usr/bin/perl
use warnings;
use strict;

use Fcntl ':seek';


open my $CSV, '<', 'donor_82_01.csv' or die "Cannot open 'donor_82_01.
+csv' because: $!";

my $pos = tell $CSV;
my %csv_data;
while ( <$CSV> ) {
        my ( $first ) = split /,+/;
        push @{ $csv_data{ $first } }, $pos;
        $pos = tell $CSV;
        }

open my $TAB, '<', 'tmp12' or die "Cannot open 'tmp12' because: $!";
open my $OUT, '>', 'tmp12_02' or die "Cannot open 'tmp12_02' because: 
+$!";

while ( <$TAB> ) {
        my ( $first, $second ) = split /\t+/;
        next unless exists $csv_data{ $second };
        for my $pos ( @{ $csv_data{ $second } } ) {
                seek $CSV, $pos, SEEK_SET or die "Cannot seek on 'dono
+r_82_01.csv' because: $!";
                print $OUT "$first,", scalar <$CSV>;
                }
        }

close $CSV;
close $TAB;
close $OUT;
[download]

Comment on Re: match two files Download Code

Replies are listed 'Best First'.
Re^2: match two files by yueli711 (Sexton) on Jun 04, 2020 at 05:02 UTC
Hello jwkrahn, Thank you so much for your useful code! Thank you again and really appreciated! `li@li-HP-$ perl match12.pl Use of uninitialized value $second in exists at match12.pl line 25, <$ +TAB> line 1. Use of uninitialized value $second in hash element at match12.pl line +26, <$TAB> line 1.` [download]	[reply] [d/l]
Re^3: match two files by jwkrahn (Abbot) on Jun 04, 2020 at 18:26 UTC
Hi! To get rid of the warning messages change the line: `my ( $first, $second ) = split /\t+/;` [download] To this: `my ( $first, $second ) = split or next;` [download]	[reply] [d/l] [select]
Re^4: match two files by yueli711 (Sexton) on Jun 05, 2020 at 02:09 UTC
Hello jwkrahn, Thank you so much for your great help! The result is actually what I wanted except missing the first line. Thank you again and really appreciated! Best, Yue I wanted: `,,AAACCTGAGCGTTTAC-1,AAACCTGAGTCGCCGT-1,AAACCTGGTAGGACAC-1,AAACCTGGTGC +CTTGG-1,AAACCTGGTTCAGCGC-1 A1CF,ENSG00000148584,0,0,0,0,0 A4GNT,ENSG00000118017,0,0,0,0,0 AARD,ENSG00000205002,0,0,0,0,0 AARS1,ENSG00000090861,0,0,0,0,0 AATK,ENSG00000181409,0,1,0,1,0 ABCA1,ENSG00000165029,0,0,0,0,0 ABCA12,ENSG00000144452,0,0,0,0,0 ABCA13,ENSG00000179869,0,0,0,0,0 ABCA6,ENSG00000154262,0,0,0,0,0 ABCA8,ENSG00000141338,0,0,0,0,0 ABCA9,ENSG00000154258,0,0,0,0,0` [download]	[reply] [d/l]
Re^5: match two files by jwkrahn (Abbot) on Jun 05, 2020 at 23:44 UTC
Re^6: match two files by yueli711 (Sexton) on Jun 06, 2020 at 01:56 UTC