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Top Forums UNIX for Dummies Questions & Answers Code for exact match to count occurrence Post 302970554 by huiyee1 on Friday 8th of April 2016 02:31:51 AM
Old 04-08-2016
Dear Scrutinizer,

Thanks for your reply.

I am trying to count the occurrences matching the content of 8th field and 9th field respectively.

Input:
Code:
field_01	field_02	field_03	field_04	field_05	field_06	field_07	field_08	field_09
TA	T	TA	T	TA	TA	TA	T	TA
CAA	CAA	CAA	C	CAA	CAA	CAA	C	CAA
CG	C	C	CG	C	C	C	C	CG
T	T	T	T	T	T	T	T	TA
AT	AT	AT	AT	A	A	A	AT	A
AT	A	A	A	AT	AT	AT	A	AT
CGA	CGA	C	CGA	C	CGA	CGA	C	CGA
GTTAC	GTTAC	G	GTTAC	GTTAC	GTTAC	G	G	GTTAC
CAT	CAT	C	CAT	C	C	C	C	CAT
AG	AG	AG	AG	AG	AG	AG	A	AG
AG	A	A	A	AG	AG	AG	A	AG

I used this command:
Code:
 awk 'BEGIN{print "count1" "\t" "count2"} NR>1 
{t=0; for(i=1; i<=7; i++) 
if($i==$8) t++; 
else if($i==$9) t++; printf("%s\t",t)} print ""}' input.txt

It does not work. There are error;
Code:
awk: cmd. line:1: BEGIN{print "count1" "\t" "count2"} NR>1 {t=0; for(i=1; i<=7; i++) if($i==$8) t++; else if($i==$9) t++; printf("%s\t",t)} print ""}
awk: cmd. line:1:                                                                                                                           ^ syntax error
awk: cmd. line:1: BEGIN{print "count1" "\t" "count2"} NR>1 {t=0; for(i=1; i<=7; i++) if($i==$8) t++; else if($i==$9) t++; printf("%s\t",t)} print ""}
awk: cmd. line:1:

The output I want is;
Code:
count1      count2
2       5
1       6
5       2
7       0
4       3
3       4
2       5
2       5
4       3
0       7
3       4

What did I do wrong? Have been trying to find out the error.
 

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STRING(3)						     Library Functions Manual							 STRING(3)

NAME
strcat, strncat, strcmp, strncmp, strcasecmp, strncasecmp, strcpy, strncpy, strlen, index, rindex - string operations SYNOPSIS
#include <strings.h> char *strcat(s, append) char *s, *append; char *strncat(s, append, count) char *s, *append; int count; strcmp(s1, s2) char *s1, *s2; strncmp(s1, s2, count) char *s1, *s2; int count; strcasecmp(s1, s2) char *s1, *s2; strncasecmp(s1, s2, count) char *s1, *s2; int count; char *strcpy(to, from) char *to, *from; char *strncpy(to, from, count) char *to, *from; int count; strlen(s) char *s; char *index(s, c) char *s, c; char *rindex(s, c) char *s, c; DESCRIPTION
These functions operate on null-terminated strings. They do not check for overflow of any receiving string. Strcat appends a copy of string append to the end of string s. Strncat copies at most count characters. Both return a pointer to the null- terminated result. Strcmp compares its arguments and returns an integer greater than, equal to, or less than 0, according as s1 is lexicographically greater than, equal to, or less than s2. Strncmp makes the same comparison but looks at at most count characters. Strcasecmp and strncasecmp are identical in function, but are case insensitive. The returned lexicographic difference reflects a conversion to lower-case. Strcpy copies string from to to, stopping after the null character has been moved. Strncpy copies exactly count characters, appending nulls if from is less than count characters in length; the target may not be null-terminated if the length of from is count or more. Both return to. Strlen returns the number of non-null characters in s. Index (rindex) returns a pointer to the first (last) occurrence of character c in string s or zero if c does not occur in the string. Set- ting c to NULL works. 4th Berkeley Distribution October 22, 1987 STRING(3)
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