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Full Discussion: Perl join two files by "common" column
Top Forums Web Development Perl join two files by "common" column Post 302494164 by yifangt on Saturday 5th of February 2011 11:17:22 PM
Old 02-06-2011
Hi Dave:
Thanks for your comments! Actually I prefer your style too, e.g. use warnings etc. I scripted another codes as:
Code:
 #!/usr/bin/perl
use strict;
#use warnings;
my %Probe_n_Seq = ();
open(FILE1, "029931_D_SequenceList_20100827.txt") || die "Can't find file $!";
    while(<FILE1>){
          chomp $_;
          my @AAA=split(/\t/, $_);
           $Probe_n_Seq{$AAA[0]}=$AAA[1];
      }
close(FILE1);

open(FILE2, "CTG_n_SCTG_AGI_Entries.txtb")        || die "Can't find file $!";
while(<FILE2>) {
   chomp $_;
    my @BBB =split (/\t/, $_);
   foreach my $key (keys (%Probe_n_Seq)) {
    if ($key =~ m/$BBB[0]\|/) {
     print $key, "\t", $Probe_n_Seq{$key},"\t",$BBB[0]."\t".$BBB[1]."\t".$BBB[2],"\n";
         } 
    } 
 }
close(FILE2);

I used the first column $AAA[0] of file1 as key of the hash, and then compare with the first column $BBB[0] of file2. If $AAA[0] contains the string $BBB[0], it means a match, as "mira_" is not the only assembly marker.
Code:
if ($key =~ m/$BBB[0]\|/)

It seems running except a small bug for
Code:
my %Probe_n_Seq = ();

which caused the warning and stopped the program. So that I have to comment the use warnings.
The code takes ~6 hours for my 2.3Ghz dual CPU + 3GB RAM (compaq machine) to run. Not sure if this could be improved for file1 has 147478 rows (15.2MB) and file2 86837 rows(7.2MB).
Actually I have another idea in my mind to reduce the work load because the iteration is 147478x86837 times. If a match is found in file1, then the matched row in file1 can be deleted so that for the next $BBB[0] in file2 does not need to search this row again. ... so that the last search is 86838 instead of 147478 loops ( when the match is in the last row, worst scenario!). The reason is each row is unique in both file. Could not figure out this by myself. Any clue is highly appreciated!
Yifang
 

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LEARN ABOUT DEBIAN

comm

COMM(1) 							   User Commands							   COMM(1)

NAME

       comm - compare two sorted files line by line

SYNOPSIS

       comm [OPTION]... FILE1 FILE2

DESCRIPTION

       Compare sorted files FILE1 and FILE2 line by line.

       With  no  options,  produce three-column output.  Column one contains lines unique to FILE1, column two contains lines unique to FILE2, and
       column three contains lines common to both files.

       -1     suppress column 1 (lines unique to FILE1)

       -2     suppress column 2 (lines unique to FILE2)

       -3     suppress column 3 (lines that appear in both files)

       --check-order
	      check that the input is correctly sorted, even if all input lines are pairable

       --nocheck-order
	      do not check that the input is correctly sorted

       --output-delimiter=STR
	      separate columns with STR

       --help display this help and exit

       --version
	      output version information and exit

       Note, comparisons honor the rules specified by `LC_COLLATE'.

EXAMPLES

       comm -12 file1 file2
	      Print only lines present in both file1 and file2.

       comm -3 file1 file2
	      Print lines in file1 not in file2, and vice versa.

AUTHOR

       Written by Richard M. Stallman and David MacKenzie.

REPORTING BUGS

       Report comm bugs to bug-coreutils@gnu.org
       GNU coreutils home page: <http://www.gnu.org/software/coreutils/>
       General help using GNU software: <http://www.gnu.org/gethelp/>
       Report comm translation bugs to <http://translationproject.org/team/>

COPYRIGHT

       Copyright (C) 2011 Free Software Foundation, Inc.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       join(1), uniq(1)

       The full documentation for comm is maintained as a Texinfo manual.  If the info and comm programs are properly installed at your site,  the
       command

	      info coreutils 'comm invocation'

       should give you access to the complete manual.

GNU coreutils 8.12.197-032bb					  September 2011							   COMM(1)
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