in reply to Re^5: 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

so suppose the first few lines of infile1 is : 

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

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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";

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

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Re^7: Compare three columns of one file with three columns of another file in perl
by NetWallah (Canon) on May 26, 2015 at 05:02 UTC
    Please use <code/> tags for code AND DATA, otherwise HTML will linearize them.

    Anyway - the data you supplied showed NO matching cases that would be printed with the code I wrote.

    After I added this line into the first file: 

    chr1    3205904    3207317

    [download]
    It correctly printed the contents expected, sot the code works as I expect.

    As suggested earlier, perl debug can help find why it does not behave as you might expect it to.

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

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[d/l]

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