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Top Forums UNIX for Dummies Questions & Answers awk split Post 302546940 by alister on Friday 12th of August 2011 02:26:52 PM
Old 08-12-2011
You can't expect characters that are used to split a string to be part of the result. If you split "1,2,3,4" on the comma, by definition the comma is not an allowed member of a field. Same goes with a bracket expression such as "[ACGT]"; splitting on such an expression forbids A, C, G, and T from occurring in a field.

Assuming I understood what were trying to do, the semicolons in your bracket expressions are incorrect. Characters in a bracket expression should not be delimited. To split on the four letters "A", "C", "G", and "T", "[ACGT]" is all that's needed. Adding those semicolons will cause splitting on semicolons as well.

Looking at your data:
Code:
>m110730_101608_00120_c100168052554400000315046108261127_s1_p0/7/29_426ACGTGCTATGCGG

If you just want to print the highlighted base sequence, and if its always preceded by the final number in the line, the following will do:
Code:
sed 's/.*[[:digit:]]//'

Or if the base sequence always begins at the 4th character past the final underscore:
Code:
sed 's/.*_...//'

Regards,
Alister

Last edited by alister; 08-12-2011 at 03:33 PM..
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SPLIT(3)								 1								  SPLIT(3)

split - Split string into array by regular expression

SYNOPSIS
array split (string $pattern, string $string, [int $limit = -1]) DESCRIPTION
Splits a $string into array by regular expression. Warning This function has been DEPRECATED as of PHP 5.3.0. Relying on this feature is highly discouraged. PARAMETERS
o $pattern - Case sensitive regular expression. If you want to split on any of the characters which are considered special by regular expressions, you'll need to escape them first. If you think split(3) (or any other regex function, for that matter) is doing some- thing weird, please read the file regex.7, included in the regex/ subdirectory of the PHP distribution. It's in manpage format, so you'll want to do something along the lines of man /usr/local/src/regex/regex.7 in order to read it. o $string - The input string. o $limit - If $limit is set, the returned array will contain a maximum of $limit elements with the last element containing the whole rest of $string. RETURN VALUES
Returns an array of strings, each of which is a substring of $string formed by splitting it on boundaries formed by the case-sensitive regular expression $pattern. If there are n occurrences of $pattern, the returned array will contain n+1 items. For example, if there is no occurrence of $pattern, an array with only one element will be returned. Of course, this is also true if $string is empty. If an error occurs, split(3) returns FALSE. EXAMPLES
Example #1 split(3) example To split off the first four fields from a line from /etc/passwd: <?php list($user, $pass, $uid, $gid, $extra) = split(":", $passwd_line, 5); ?> Example #2 split(3) example To parse a date which may be delimited with slashes, dots, or hyphens: <?php // Delimiters may be slash, dot, or hyphen $date = "04/30/1973"; list($month, $day, $year) = split('[/.-]', $date); echo "Month: $month; Day: $day; Year: $year<br /> "; ?> NOTES
Note As of PHP 5.3.0, the regex extension is deprecated in favor of the PCRE extension. Calling this function will issue an E_DEPRECATED notice. See the list of differences for help on converting to PCRE. Tip split(3) is deprecated as of PHP 5.3.0. preg_split(3) is the suggested alternative to this function. If you don't require the power of regular expressions, it is faster to use explode(3), which doesn't incur the overhead of the regular expression engine. Tip For users looking for a way to emulate Perl's @chars = split('', $str) behaviour, please see the examples for preg_split(3) or str_split(3). SEE ALSO
preg_split(3), spliti(3), str_split(3), explode(3), implode(3), chunk_split(3), wordwrap(3). PHP Documentation Group SPLIT(3)
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