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Parsing a list of data

 
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# 1  
Old 08-06-2012
Parsing a list of data
Hi
I have a vcf file with 20000 lines, it looks like this-
Code:
23	122691	.	C	1345.09	PASS
33	122961	.	C	833.45	PASS
43	122970	.	A	689.75	PASS
53	123009	.	T	118.99	PASS
63	123033	.	T	46.85	PASS
73	123042	.	A	127.51	PASS
83	123060	.	T	299.64	PASS
93	123081	.	T	299.64	PASS
103	123105	.	C	210.83	PASS
113	123108	.	G	139.65	PASS
123	123147	.	A	132.79	PASS
133	123162	.	A	120.25	PASS
143	123171	.	G	174.31	SnpCluster
153	123177	.	C	109.46	SnpCluster
163	123180	.	G	146.46	SnpCluster
173	123282	.	A	10.22	LowQual;SnpCluster
183	123285	.	A	15.92	LowQual;SnpCluster
193	123288	.	G	15.92	LowQual;SnpCluster
203	123300	.	A	1327.57	PASS
213	123301	.	G	955.37	PASS
223	123321	.	A	708.37	PASS
233	123363	.	G	131.35	PASS
243	123366	.	A	742.72	PASS
253	123407	.	C	574.47	SnpCluster
263	123408	.	T	574.47	SnpCluster
273	123411	.	A	696.24	SnpCluster
283	123420	.	G	89.09	PASS
293	123426	.	A	690.57	PASS
303	123474	.	A	59.45	PASS
313	123477	.	C	576.22	PASS
323	123489	.	G	396.59	PASS
333	123651	.	C	79.36	PASS
343	123705	.	C	908.33	PASS
353	436405	.	C	969.24	PASS
363	436472	.	G	969.24	PASS
373	436614	.	C	1052.76	PASS
383	436684	.	A	718.68	PASS
393	436748	.	C	676.92	PASS
403	436760	.	T	718.68	PASS
413	436798	.	A	927.48	PASS

I want to filter this file based on the values/ranges in column 2. For example, in a new file I do not want lines with values 123171-123407, and 123651-436748 in column2. Please suggest any simple unix command.

Thanks
Last edited by Scott; 08-06-2012 at 06:59 PM.. Reason: Please use code tags, and a meaningful subject title to describe your problem. Thank you.
# 2  
Old 08-06-2012
Code:
nawk '!($2>=123171 && $2<=123407 && $2>=123651 && $2<=436748)' myFile

# 3  
Old 08-07-2012
Shouldn't there be a "logical or" || as the middle operator?
# 4  
Old 08-07-2012
Thanks! It worked using || as middle operator.
 
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