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  • How can I extract each APAsite possibility from this table?

    Hello,

    I have an output from APATrap package, which gives back the predicted APA sites from samples. I need to make a list from all the possibles APAs to cross it with miRNAs database and get known if there is a match. The problem is a have a huges lists from 16 samples, and I need a way to automatize this task for reproducibility.

    I have this summed up table:

    Predicted_APA.TOTAL Loci.TOTAL

    41867799,41867388,41866990 chr17:41866927-41867904

    And I need something like this:

    CHR Loci.UTR.TOTAL Locus initial Locus Final

    chr17 41866927-41867799 41866927 41867799
    chr17 41866927-41867388 41866927 41867388
    chr17 41866927-41866990 41866927 41866990

    Do you know any tip or clue to do it for 16 samples with 1000 results each one?

    Thanks in advance, and sorry if my question isn't appropriate. I will answer any question for further people in the same situation.
    Beginner @ RNA-Seq, R programming, Linux, Python.-

    Please be patients!

  • #2
    I got this answer from another forum, so I add it here in case someone needs it.

    input:
    $cat test.txt

    Predicted_APA.TOTAL Loci.TOTAL
    41867799,41867388,41866990 chr17:41866927-41867904
    output:
    $awk -v FS='[-:\t]' -v OFS="\t" ' NR != 1 {split($1,a,","); for (i in a) {print $2,$3"-"a[i],$3,a[i]}}' test.txt

    chr17 41866927-41867799 41866927 41867799
    chr17 41866927-41867388 41866927 41867388
    chr17 41866927-41866990 41866927 41866990
    Beginner @ RNA-Seq, R programming, Linux, Python.-

    Please be patients!

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