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Top Forums Shell Programming and Scripting Outputting characters after a given string and reporting the characters in the row below --sed Post 303028719 by Don Cragun on Sunday 13th of January 2019 10:23:36 PM
Old 01-13-2019
This is probably easier to read and produces the same output:
Code:
awk '
BEGIN {	String = "GCATGAAAACATACA"
	StringLen = length(String)
}
/^@/ {	getline CodonLine
	getline
	getline QualityLine
	if(spot = index(CodonLine, String))
		printf("Codon:\t%s\tQuality Score:\t%s\n",
		    substr(CodonLine, spot + StringLen, 3),
		    substr(QualityLine, spot + StringLen, 3))
}' file

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GETDELIM(3)						   BSD Library Functions Manual 					       GETDELIM(3)

NAME
getdelim, getline -- read a delimited record from a stream LIBRARY
Standard C Library (libc, -lc) SYNOPSIS
#include <stdio.h> ssize_t getdelim(char ** restrict lineptr, size_t * restrict n, int delimiter, FILE * restrict stream); ssize_t getline(char ** restrict lineptr, size_t * restrict n, FILE * restrict stream); DESCRIPTION
The getdelim() function reads from the stream until it encounters a character matching delimiter, storing the input in *lineptr. The buffer is NUL-terminated and includes the delimiter. The delimiter character must be representable as an unsigned char. If *n is non-zero, then *lineptr must be pre-allocated to at least *n bytes. The buffer should be allocated dynamically; it must be possible to free(3) *lineptr. getdelim() ensures that *lineptr is large enough to hold the input, updating *n to reflect the new size. The getline() function is equivalent to getdelim() with delimiter set to the newline character. RETURN VALUES
The getdelim() and getline() functions return the number of characters read, including the delimiter. If no characters were read and the stream is at end-of-file, the functions return -1. If an error occurs, the functions return -1 and the global variable errno is set to indi- cate the error. The functions do not distinguish between end-of-file and error, and callers must use feof(3) and ferror(3) to determine which occurred. EXAMPLES
The following code fragment reads lines from a file and writes them to standard output. char *line = NULL; size_t linesize = 0; ssize_t linelen; while ((linelen = getline(&line, &linesize, fp)) != -1) fwrite(line, linelen, 1, stdout); if (ferror(fp)) perror("getline"); ERRORS
[EINVAL] lineptr or n is a NULL pointer. [EOVERFLOW] More than SSIZE_MAX characters were read without encountering the delimiter. The getdelim() and getline() functions may also fail and set errno for any of the errors specified in the routines fflush(3), malloc(3), read(2), stat(2), or realloc(3). SEE ALSO
ferror(3), fgets(3), fopen(3) STANDARDS
The getdelim() and getline() functions conform to IEEE Std 1003.1-2008 (``POSIX.1''). BSD
June 30, 2010 BSD
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