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.
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gandrescabrera
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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
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