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Top Forums UNIX for Beginners Questions & Answers Grep or awk a unique and specific word across many fields Post 302999191 by daashti on Thursday 15th of June 2017 06:45:47 AM
Old 06-15-2017
it shouldn't as the next filed has hetero. it should look for all fields after the 6th column.

I am trying to create to separate files one with hetero and one with homo. if its easier to code that way.

input:
Code:
CHR	START-SNP	END-SNP	REF	ALT	PATIENT1	PATIENT2	PATIENT3	PATIENT4
chr1	69511	69511	A	G	homo	hetero	homo	hetero
chr2	69513	69513	T	C	.	hetero	homo	hetero
chr3	69814	69814	G	C	.	.	homo	homo
chr4	69815	69815	C	A	hetero	.	.	hetero

when grep/awk for hetero
output 1:
Code:
CHR	START-SNP	END-SNP	REF	ALT	PATIENT1	PATIENT2	PATIENT3	PATIENT4
chr4	69815	69815	C	A	hetero	.	.	hetero

when grep/awk for homo
output 2:
Code:
CHR	START-SNP	END-SNP	REF	ALT	PATIENT1	PATIENT2	PATIENT3	PATIENT4
chr3	69814	69814	G	C	.	.	homo	homo

BTW the file I have has many PATIENT1-10000 columns
 

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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specifed in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. JOIN(1)
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