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Full Discussion: Reverse complement
Top Forums UNIX for Dummies Questions & Answers Reverse complement Post 302950517 by RudiC on Sunday 26th of July 2015 02:39:29 AM
Old 07-26-2015
sed approach (not necessarily easier to explain...):
Code:
sed '/>/n; y/ATCG/TAGC/;s/^.*$/X&X/;:x;s/\(X.\)\(.*\)\(.X\)/\3\2\1/;tx;s/X//g' file
>GHL8OVD01CMQVT SHORT1
ACATCAA
>GHL8OVD01CMQVT SHORT2
ACATCAA

or, if you have GNU sed with its extensions:
Code:
sed '/>/n; y/ATCG/TAGC/;s/^/echo /;s/$/ | rev/;e' file

This User Gave Thanks to RudiC For This Post:
 

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STRCSPN(3)						   BSD Library Functions Manual 						STRCSPN(3)

NAME
strcspn -- span the complement of a string LIBRARY
Standard C Library (libc, -lc) SYNOPSIS
#include <string.h> size_t strcspn(const char *s1, const char *s2); DESCRIPTION
The strcspn() function spans the initial part of the null-terminated string s1, as long as the characters from s1 do not occur in string s2 (it spans the complement of s2). In other words, it computes the string array index in s1 of the first character of s1 which is also in s2, else the index of the first null character. RETURN VALUES
The strcspn() function returns the number of characters spanned. SEE ALSO
memchr(3), strchr(3), strpbrk(3), strrchr(3), strsep(3), strspn(3), strstr(3), strtok(3) STANDARDS
The strcspn() function conforms to ISO/IEC 9899:1990 (``ISO C90''). BSD
June 4, 1993 BSD
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