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.

In reply to Re^6: Compare three columns of one file with three columns of another file in perl by anonym
in thread Compare three columns of one file with three columns of another file in perl by anonym

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