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Top Forums UNIX for Dummies Questions & Answers Help with finding matching position on strings Post 302507281 by Corona688 on Wednesday 23rd of March 2011 11:35:01 AM
Old 03-23-2011
What is your system? What is your shell?

---------- Post updated at 09:24 AM ---------- Previous update was at 09:18 AM ----------

dna.awk:
Code:
{
        LINE++;
        for(N=0; N<(length($0)-length(STR)); N++)
        if(STR == substr($0, N, length(STR)))
                printf("Line %d, position %d\n", LINE, N);
}

Code:
$ awk -f dna.awk -v STR="GAT" dnafile
Line 1, position 10
Line 3, position 10
Line 3, position 46
$

---------- Post updated at 09:35 AM ---------- Previous update was at 09:24 AM ----------

Slight modification to dna.awk:
Code:
{
        LINE++;
        for(N=0; N<(length($0)-length(STR)); N++)
        if(STR == substr($0, N, length(STR)))
                printf("Line %d, %d-%d\n", LINE, N, N+length(STR));
}

 

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BM(PUBLIC)																BM(PUBLIC)

NAME
bm - search a file for a string SYNOPSIS
/usr/public/bm [ option ] ... [ strings ] [ file ] DESCRIPTION
Bm searches the input files (standard input default) for lines matching a string. Normally, each line found is copied to the standard out- put. It is blindingly fast. Bm strings are fixed sequences of characters: there are no wildcards, repetitions, or other features of regu- lar expressions. Bm is also case sensitive. The following options are recognized. -x (Exact) only lines matched in their entirety are printed -l The names of files with matching lines are listed (once) separated by newlines. -c Only a count of the number of matches is printed -e string The string is the next argument after the -e flag. This allows strings beginning with '-'. -h No filenames are printed, even if multiple files are searched. -n Each line is preceded by the number of characters from the beginning of the file to the match. -s Silent mode. Nothing is printed (except error messages). This is useful for checking the error status. -f file The string list is taken from the file. Unless the -h option is specified the file name is shown if there is more than one input file. Care should be taken when using the charac- ters $ * [ ^ | ( ) and in the strings (listed on the command line) as they are also meaningful to the Shell. It is safest to enclose the entire expression argument in single quotes ' '. Bm searches for lines that contain one of the (newline-separated) strings, using the Boyer-Moore algorithm. It is far superior in terms of speed to the grep (egrep, fgrep) family of pattern matchers for fixed-pattern searching, and its speed increases with pattern length. SEE ALSO
grep(1) DIAGNOSTICS
Exit status is 0 if any matches are found, 1 if none, 2 for syntax errors or inaccessible files. AUTHOR
Peter Bain (pdbain@wateng), with modifications suggested by John Gilmore BUGS
Only 100 patterns are allowed. Patterns may not contain newlines. If a line (delimited by newlines, and the beginning and end of the file) is longer than 8000 charcters (e.g. in a core dump), it will not be completely printed. If multiple patterns are specified, the order of the ouput lines is not necessarily the same as the order of the input lines. A line will be printed once for each different string on that line. The algorithm cannot count lines. The -n and -c work differently from fgrep. The -v, -i, and -b are not available. 4th Berkeley Distribution 8 July 1985 BM(PUBLIC)
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