Re^4: Compare three columns of one file with three columns of another file in perl

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Re^5: Compare three columns of one file with three columns of another file in perl by NetWallah (Canon) on May 26, 2015 at 03:25 UTC
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]
Re^6: Compare three columns of one file with three columns of another file in perl by anonym (Acolyte) on May 26, 2015 at 03:37 UTC
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]
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	[reply] [d/l]