I have had to split by fasta genome into chunks to speed up annotation using maker as we did not have mpi up and chromosomes were very large. I need to add the last value in the string of the first column to columns 4 and 5 to correct the starting and finish positions. I need to do this to multiple files so ideally parse the value rather than manually enter the value but even that would be helpful. I think this should be quite easy awk but still not familiar with it, any ideas?
Examples line:
Chr13_pilon_pilon_8000000 maker gene 1257 1527 . + . ID=maker-Chr13_pilon_pilon_8000000-exonerate_est2genome-gene-0.0;Name=evgtrinLocGG_7725c278g1t1-gene
Examples output:
Chr13_pilon_pilon_8000000 maker gene 8001257 8001527 . + . ID=maker-Chr13_pilon_pilon_8000000-exonerate_est2genome-gene-0.0;Name=evgtrinLocGG_7725c278g1t1-gene
•
written
by
rob234king
if the value you need to add to columns 4 and 5 is always behind a "_" character in the first column, then this perl code should work:
perl -lane 'if (/^\S+_(\d+)/) { $F[3] += $1; $F[4] += $1; print join "\t", @F}' input.txt
not caring about the number of total columns:
awk '{n=split($1,a,"_"); $4+=a[n]; $5+=a[n]; print}' input.txt
not caring about the number of total columns, plus considering that both input and output are tabulated:
awk 'FS=OFS="\t"{n=split($1,a,"_"); $4+=a[n]; $5+=a[n]; print}' input.txt
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