in reply to Re: compare two files on the basis of Two IDs
in thread compare two files on the basis of Two IDs

Hi, Thanks for your reply. I tried to print the result for file 1, but not for file 2. I am trying the code, but not worked for me. 

#!/usr/bin/perl
#use warnings; 
#use strict;
#use Data::Dumper;

my $file1 = $ARGV[0];
open($infile1,$file1);
my $file2 = $ARGV[1];
open($infile2,$file2);

my %file2_hash;

while (my $line = <$infile2>)
{
   next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof
+)
   
   my ($key, $value1, $value2) = split /\s+/, $line; # use better "nam
+es" I have
                                           # no idea of what a chr col
+ means
   $file2_hash{"$key:$value1:$value2"} = 1;
}
close $infile2;

while (my $line = <$infile1>)
{
   chomp $line;  #so that output with E or M can be on same line
   next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof
+)
   
   my ($chr, $value1) = split /\s+/,$line;
   
   if (exists $file2_hash{"$chr:$value1"} or exists $file2_hash{"$chr:
+$value2"} )
   {
      print "$line\tE\n";  # match exists with file 1
   }
   else
   {
      print "$line\tM\n";  # match does NOT exist with file 1
   }
}

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Re^3: compare two files on the basis of Two IDs
by marinersk (Priest) on Sep 28, 2016 at 03:05 UTC

    This code works for me. Is there something wrong with the output?

    a.dat:

    chr17    69112551
chr1    67058869
chr7    151046672
chr7    151047369
chr1    66953654

    [download]

    b.dat:

    chr1    66953622    66953654
chr1    67200451    67200472
chr1    67200475    67200478
chr1    67058869    67058880
chr1    67058881    67058885
chr1    67058887    67058895

    [download]

    Results:

    S:\Steve\PerlMonks>compare.pl a.dat b.dat
chr17   69112551        M
chr1    67058869        M
chr7    151046672       M
chr7    151047369       M
chr1    66953654        M

S:\Steve\PerlMonks>

    [download]

[reply]
[d/l]
[select]
      yes, Its a wrong code. It is giving the result with all M, but not E.. May be it is not considering the condition to print Es. Could you please help me in this. In original file, we have several entries, may give the Es.. Pleas have a look on the code

[reply]
        Marshall wrote:
        "I couldn't see any way to get an "E" with your test data, so I added some extra data to my test cases. In the future, it is best if you can provide an example "desired output" that demo's the basic decisions which need to be made.
        show an example output and explain clearly how you arrived at that result.
[reply]

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