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Old 03-22-2017, 01:41 AM   #1
Location: Sweden

Join Date: May 2014
Posts: 19
Default Collapsing gene names based on partial string overlap

I have a long list of gene names with corresponding read counts. I'm mainly interested that the tRNAs with an identical anticodon are collapsed and the sum of their read counts is calculated.

Therefore, something like:
collapse names in lines containing "tRNA" based on the perfect match of the last 6 characters in the gene name (e.g. GluCTC) and sum up corresponding read counts. The new gene name can be "tRNA-" followed by the aforementioned 6 characters (e.g. tRNA-GluCTC)

The input (tab-delimited) looks like this:
Gm26624	                5761
Bre                     5658
chr10.tRNA90-GluCTC	5573
chr3.tRNA303-GluCTC	5558
chr1.tRNA709-GluCTC	5489
chr1.tRNA706-GlyGCC	4891
chr1.tRNA704-GlyGCC	4838
chr1.tRNA702-GlyGCC	4796
chr13.tRNA110-GlyGCC	4753
Gm13247	                4105
Rny3	                3736
chr1.tRNA485-LysTTT	3548
Rn7s2	                3385
chr19.tRNA107-LysTTT	3363
Any ideas how to do this? Awk?
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