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Full Discussion: awk split
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..
This User Gave Thanks to alister For This Post:
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LEARN ABOUT OPENSOLARIS

fmt

fmt(1)								   User Commands							    fmt(1)

NAME

       fmt - simple text formatters

SYNOPSIS

       fmt [-cs] [-w width | -width] [inputfile]...

DESCRIPTION

       fmt  is a simple text formatter that fills and joins lines  to produce output lines of (up to) the number of characters specified in the -w
       width option. The default  width is 72. fmt concatenates the inputfiles listed as arguments. If none are given, fmt formats text  from  the
       standard input.

       Blank lines are preserved in the output, as is the spacing between words. fmt does not fill nor split lines beginning with a `.' (dot), for
       compatibility with nroff(1). Nor does it fill or split a set of contiguous non-blank lines which is determined to be  a	mail  header,  the
       first line of which must begin with "From".

       Indentation is preserved in the output, and input lines with differing indentation are not joined (unless -c is used).

       fmt can also be used as an in-line text filter for vi(1). The  vi command:

       !}fmt

       reformats the text between the cursor location and the end of the paragraph.

OPTIONS

       -c		    Crown  margin  mode.  Preserve the indentation of the first two lines within a paragraph, and align the left margin of
			    each subsequent line with that of the second line. This is useful for tagged paragraphs.

       -s		    Split lines only. Do not join short lines to form longer ones. This prevents sample lines of code, and other such for-
			    matted text, from being unduly combined.

       -w width | -width    Fill output lines to up to	width columns.

OPERANDS

       inputfile    Input file.

ENVIRONMENT VARIABLES

       See environ(5) for a description of the LC_CTYPE environment variable that affects the execution of fmt.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWcsu			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       nroff(1), vi(1), attributes(5), environ(5)

NOTES

       The -width option is acceptable for BSD compatibility, but it may go away in future releases.

SunOS 5.11							    9 May 1997								    fmt(1)
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