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Top Forums UNIX for Dummies Questions & Answers Selectively extracting entries from FASTA file Post 302960033 by Don Cragun on Monday 9th of November 2015 08:44:58 PM
Old 11-09-2015
You mean something like:
Code:
awk -v search1="ccccta" -v search2="ccccccccc" '$1~/^>/ {buf=sep=""; found=0} found==1 {print; next} {buf=buf sep $0; sep=RS} $0~search1 && $0~search2 {print but; found=1}' infile > outfile1

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STRTOK(3)						   BSD Library Functions Manual 						 STRTOK(3)

NAME
strtok, strtok_r -- string tokens LIBRARY
Standard C Library (libc, -lc) SYNOPSIS
#include <string.h> char * strtok(char *restrict str, const char *restrict sep); char * strtok_r(char *restrict str, const char *restrict sep, char **restrict lasts); DESCRIPTION
This interface is obsoleted by strsep(3). The strtok() function is used to isolate sequential tokens in a null-terminated string, str. These tokens are separated in the string by at least one of the characters in sep. The first time that strtok() is called, str should be specified; subsequent calls, wishing to obtain further tokens from the same string, should pass a null pointer instead. The separator string, sep, must be supplied each time, and may change between calls. The implementation will behave as if no library function calls strtok(). The strtok_r() function is a reentrant version of strtok(). The context pointer last must be provided on each call. The strtok_r() function may also be used to nest two parsing loops within one another, as long as separate context pointers are used. The strtok() and strtok_r() functions return a pointer to the beginning of each subsequent token in the string, after replacing the token itself with a NUL character. When no more tokens remain, a null pointer is returned. EXAMPLES
The following uses strtok_r() to parse two strings using separate contexts: char test[80], blah[80]; char *sep = "\/:;=-"; char *word, *phrase, *brkt, *brkb; strcpy(test, "This;is.a:test:of=the/string\tokenizer-function."); for (word = strtok_r(test, sep, &brkt); word; word = strtok_r(NULL, sep, &brkt)) { strcpy(blah, "blah:blat:blab:blag"); for (phrase = strtok_r(blah, sep, &brkb); phrase; phrase = strtok_r(NULL, sep, &brkb)) { printf("So far we're at %s:%s ", word, phrase); } } SEE ALSO
memchr(3), strchr(3), strcspn(3), strpbrk(3), strrchr(3), strsep(3), strspn(3), strstr(3), wcstok(3) STANDARDS
The strtok() function conforms to ISO/IEC 9899:1990 (``ISO C90''). BUGS
The System V strtok(), if handed a string containing only delimiter characters, will not alter the next starting point, so that a call to strtok() with a different (or empty) delimiter string may return a non-NULL value. Since this implementation always alters the next starting point, such a sequence of calls would always return NULL. AUTHORS
Wes Peters, Softweyr LLC: <wes@softweyr.com> Based on the FreeBSD 3.0 implementation. BSD
November 27, 1998 BSD
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