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  • 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:
    Code:
    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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