Shell Programming and Scripting

Hi,

I am not sure how well I can explain this.. Below is the file which I want to perform the code on.. Column 2 are my stop sites and column 3 are my start site.. For every gene I need to look at my starts(column3) and add +10,000 to it only if there is no gene when we move upstream 10,000( which mean the next gene stop site(column2) should not coincide with it).

Code:

chr1	879582	894679	NOC2L
chr1	934341	935552	HES4
chr1	1007125	1009687	RNF223
chr1	1017197	1051736	C1orf159
chr1	1138887	1142089	TNFRSF18
chr1	1146705	1149548	TNFRSF4
chr1	1152287	1167447	SDF4
chr1	1177825	1182102	FAM132A
chr1	1189291	1209234	UBE2J2
chr1	1227763	1243269	ACAP3
chr1	1246964	1260046	CPSF3L
chr1	1270657	1284492	DVL1
chr1	1288070	1293915	MXRA8

For the first gene NOC2L start site is 894679 when I try to add +10,000 its going to be 904679, which does not coincide with the next gene stop site( 934341). If it coincides then that row should be left as it is

output

Code:

chr1	879582	894679	NOC2L
chr1 894680 904679 NOC2L_1
chr1	934341	935552	HES4
chr1 935553 945553 HES4_1

Let me know if I am not clear..

Thanks,

Hi,

try this:

Code:

cat YOURFILE.txt |awk -F " " '{if ($2 == a ) {print $0}; a=$3 + 10001;}'

Moderator's Comments:

Use code tags instead of quote tags, thank you

Try:

Code:

awk 'v<$2{print p}1; {$2=$3+1; v=$3+=10000; $4=$4"_1"; p=$0} END{print p}' infile

I don't know if END{print p} is necessary, otherwise you can leave that out..

Great it worked...

Thanks,