in reply to Re^2: Compare three columns of one file with three columns of another file in perl
in thread Compare three columns of one file with three columns of another file in perl

This line in my code has a typo .. should be corrected to meet your reaquirements : 
   $_->[3] eq $two[4] 
   # should be:
   $_->[2] eq $two[4]

[download]
The code was intended as a style and structure guide, not necessarily a complete solution.

        "You're only given one little spark of madness. You mustn't lose it."         - Robin Williams

  • Comment on Re^3: Compare three columns of one file with three columns of another file in perl
  • Download Code

Replies are listed 'Best First'.
Re^4: Compare three columns of one file with three columns of another file in perl
by anonym (Acolyte) on May 26, 2015 at 03:11 UTC

    Thanks but it prints nothing to the standard output

[reply]
      Please post a small sample of data from each file .. including one or two lines where you expect it to print, and one or two where it should NOT print. ALternatively, learn to use perl debug, to diagnose the issue.

              "Despite my privileged upbringing, I'm actually quite well-balanced. I have a chip on both shoulders."         - John Nash

[reply]

        so suppose the first few lines of infile1 is : 

        chr10   40095550        40096075
chr10   40102275        40102575
chr10   40139575        40140100
chr10   40145000        40146125

        [download]
        and the first few lines of infile2 is 
        chr1    mm10_knownGene  exon    3205904 3207317 0.000000        -     
+  .       gene_id "uc007aet.1"; transcript_id "uc007aet.1"; 
chr1    mm10_knownGene  exon    3213439 3215632 0.000000        -     
+  .       gene_id "uc007aet.1"; transcript_id "uc007aet.1"; 
chr1    mm10_knownGene  stop_codon      3216022 3216024 0.000000      
+  -       .       gene_id "uc007aeu.1"; transcript_id "uc007aeu.1"; 
chr1    mm10_knownGene  CDS     3216025 3216968 0.000000        -     
+  2       gene_id "uc007aeu.1"; transcript_id "uc007aeu.1";

        [download]
        the columns chr, start,end all three should match between these two files.print out the matched ones.Thanks.

[reply]
[d/l]
[select]

In Section Seekers of Perl Wisdom