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Length of a segment based on coordinates

 
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# 1  
Old 10-26-2012
Length of a segment based on coordinates
Hi,

I would like to have the length of a segment based on coordinates of its parts.

Example input file:
Code:
chr11	genes_good3.gtf	aggregate_gene	1	100 gene1
chr11	genes_good3.gtf	exonic_part	1	60
chr11	genes_good3.gtf	exonic_part	70	100
chr11	genes_good3.gtf	aggregate_gene	200	1000 gene2
chr11	genes_good3.gtf	exonic_part	200	300
chr11	genes_good3.gtf	exonic_part	500	800
chr11	genes_good3.gtf	exonic_part	900	1000

Desired output file:
Code:
gene1 90
gene2 500

Thanks in advance!
Last edited by Scott; 10-26-2012 at 09:10 AM.. Reason: Code tags
# 2  
Old 10-26-2012
Try:
Code:
awk '/aggregate_gene/{n=$6}/exonic_part/{a[n]+=($5-$4)}END{for (n in a) print n,a[n]}' input

# 3  
Old 10-26-2012
Thanks a lot! It works.
 
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