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  • cmccabe
    Senior Member
    • Jul 2012
    • 355

    #1

    awk, perl, or sed to parse delins

    I have a special case that for awk, perl, or sed to parse but I do not have the skill nor do I know where to start. Trying to create a final output file (indel_parse.txt) that is created from using some information from each of the two files (attached).

    Basically, there is information needed in each file that is combined into an indel_parse.txt file. Thank you .

    The header is skipped:

    1. 4 zeros after the NC_ (not always the case) and the digits before the . [column 1 in indel_name.txt] - NM_004004.5:c.34_35delGGinsT

    2. g. ### (before underscore) _### (# after the _) [column 3 in indel_position.txt] - NC_000013.10:g.20763686_20763687delinsA

    3. letters after "del"

    4. letters after "ins”

    indel_parse.txt
    13 20763686 20763687 GG T

    Thank you .
    Attached Files

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