awk split Post: 302546940

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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

08-12-2011

Registered User

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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LEARN ABOUT DEBIAN

plan9-split

SPLIT(1)						      General Commands Manual							  SPLIT(1)

NAME

       split - split a file into pieces

SYNOPSIS

       split [ option ...  ] [ file ]

DESCRIPTION

       Split reads file (standard input by default) and writes it in pieces of 1000 lines per output file.  The names of the output files are xaa,
       xab, and so on to xzz.  The options are

       -n n   Split into n-line pieces.

       -l n   Synonym for -n n, a nod to Unix's syntax.

       -e expression
	      File divisions occur at each line that matches a regular expression; see regexp(7).  Multiple -e options may appear.   If  a  subex-
	      pression	of  expression is contained in parentheses (...), the output file name is the portion of the line which matches the subex-
	      pression.

       -f stem
	      Use stem instead of x in output file names.

       -s suffix
	      Append suffix to names identified under -e.

       -x     Exclude the matched input line from the output file.

       -i     Ignore case in option -e; force output file names (excluding the suffix) to lower case.

SOURCE

       /src/cmd/split.c

SEE ALSO

       sed(1), awk(1), grep(1), regexp(7)

																	  SPLIT(1)

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