Question

I have a file with the following fields (and an example value to the right):

hg18.ensGene.bin 0
hg18.ensGene.name ENST00000371026
hg18.ensGene.chrom chr1
hg18.ensGene.strand -
hg18.ensGene.txStart 67051161
hg18.ensGene.txEnd 67163158
hg18.ensGene.exonStarts 67051161,67060631,67065090,67066082,67071855,67072261,67073896,67075980,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932,
hg18.ensGene.exonEnds 67052451,67060788,67065317,67066181,67071977,67072419,67074048,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158,
hg18.ensGene.name2 ENSG00000152763
hg18.ensGene.exonFrames 0,2,0,0,1,2,0,0,1,1,1,2,1,2,0,2,0,

This is a shortened version of the file:

0 ENST00000371026 chr1 - 67051161 67163158 67051161,67060631,67065090,67066082,67071855,67072261,67073896,67075980,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932, 67052451,67060788,67065317,67066181,67071977,67072419,67074048,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158, ENSG00000152763 0,2,0,0,1,2,0,0,1,1,1,2,1,2,0,2,0, uc009waw.1,uc009wax.1,uc001dcx.1,
0 ENST00000371023 chr1 - 67075869 67163055 67075869,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932, 67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163055, ENSG00000152763 0,1,1,1,2,1,2,0,2,0, uc001dcy.1
0 ENST00000395250 chr1 - 67075991 67163158 67075991,67076022,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932, 67076018,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158, ENSG00000152763 0,0,1,1,1,2,0,-1,-1,-1,-1, n/a

I need to sum the difference of the exon starts and ends for example:

hg18.ensGene.exonStarts    67051161,67060631,67065090,67066082,67071855,67072261,67073896,67075980,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932,
hg18.ensGene.exonEnds    67052451,67060788,67065317,67066181,67071977,67072419,67074048,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158,

difference:

1290,157,227,99,122,158,152,87,203,195,156,140,157,113,185,175,226

sum (hg18.ensGene.exonLenSum):

3842

And I would like the output to have the following fields:

hg18.ensGene.name
hg18.ensGene.name2
hg18.ensGene.exonLenSum

such as this:

ENST00000371026 ENST00000371023 3842

I would like to do this with one awk script for all lines in the input file. How can I do this? This is useful for calculating exon lengths, say for a RPMK (Reads Per Kilobase exon Model per million mapped reads) calculation.

Answer 1

so ross$ awk -f gene.awk gene.dat
ENST00000371026 ENSG00000152763 3842
ENST00000371023 ENSG00000152763 1645
ENST00000395250 ENSG00000152763 1622
so ross$ cat gene.awk
/./ {
  name = $2
  name2 = $9
  s = $7
  e = $8
  sc = split(s, sa, ",")
  ec = split(e, ea, ",")
  if (sc != ec) {
    print "starts != ends ", name, name2, sc, ec
  }
  diffsum = 0
  for(i = 1; i <= sc; ++i) {
    diffsum += ea[i] - sa[i]
  }
  print name, name2, diffsum
}