awk for loop to break up file into chunks -


i have large file break chunks field 2. field 2 ranges in value 0 250 million. 

1 10492 rs55998931 c t 6 7 3 3 - 0.272727272727273 0.4375 1 13418 . g 6 1 2 3 ddx11l1 0.25 0.0625 1 13752 . t c 4 4 1 3 ddx11l1 0.153846153846154 0.25 1 13813 . t g 1 4 0 1 ddx11l1 0.0357142857142857 0.2 1 13838 rs200683566 c t 1 4 0 1 ddx11l1 0.0357142857142857 0.2

i want field 2 broken intervals of 50,000, overlapping 2,000. example, first 3 awk commands like:

awk '$1=="1" && $2>=0 && $2<=50000{print$0}' highalt.lowalt.allelecounts.filteredformissing.freq > chr1.0kb.50kb  awk '$1=="1" && $2>=48000 && $2<=98000{print$0}' highalt.lowalt.allelecounts.filteredformissing.freq > chr1.48kb.98kb  awk '$1=="1" && $2>=96000 && $2<=146000{print$0}' highalt.lowalt.allelecounts.filteredformissing.freq > chr1.96kb.146kb

i know there's way can using loop variables , j. can me out?

awk '$1=="1"{n=int($2/48000); print>("chr1." (48*n) "kb." (48*n+50) "kb");n--; if (n>=0 && $2/1000<=48*n+50) print>("chr1." (48*n) "kb." (48*n+50) "kb");}' highalt.lowalt.allelecounts.filteredformissing.freq

or spread out on multiple lines:

awk '$1=="1"{     n=int($2/48000)     print>("chr1." (48*n) "kb." (48*n+50) "kb")     n--     if (n>=0 && $2/1000<=48*n+50)         print>("chr1." (48*n) "kb." (48*n+50) "kb") }' highalt.lowalt.allelecounts.filteredformissing.freq

how works

  • $1=="1"{

    this selects lines first field 1. (you didn't mention in text code applied restriction.

  • n=int($2/48000)

    this computes bucket line belongs in.

  • print>("chr1." (48*n) "kb." (48*n+50) "kb")

    this writes line appropriate file

  • n--

    this decrements bucket number

  • if (n>=0 && $2/1000<=48*n+50) print>("chr1." (48*n) "kb." (48*n+50) "kb")

    if line fits within overlapping range of previous bucket, write bucket also.

  • }

    this closes group started selecting $1=="1".


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