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Full Discussion: Stops and start
Top Forums Shell Programming and Scripting Stops and start Post 302625305 by Diya123 on Tuesday 17th of April 2012 02:31:10 PM
Old 04-17-2012
Stops and start

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,
 

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COLRM(1)						    BSD General Commands Manual 						  COLRM(1)

NAME
colrm -- remove columns from a file SYNOPSIS
colrm [start [stop]] DESCRIPTION
The colrm utility removes selected columns from the lines of a file. A column is defined as a single character in a line. Input is read from the standard input. Output is written to the standard output. If only the start column is specified, columns numbered less than the start column will be written. If both start and stop columns are spec- ified, columns numbered less than the start column or greater than the stop column will be written. Column numbering starts with one, not zero. Tab characters increment the column count to the next multiple of eight. Backspace characters decrement the column count by one. ENVIRONMENT
The LANG, LC_ALL and LC_CTYPE environment variables affect the execution of colrm as described in environ(7). EXIT STATUS
The colrm utility exits 0 on success, and >0 if an error occurs. SEE ALSO
awk(1), column(1), cut(1), paste(1) HISTORY
The colrm command appeared in 3.0BSD. BSD
August 4, 2004 BSD
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