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Top Forums Shell Programming and Scripting Extract text between two character positions Post 302594442 by Twinklefingers on Tuesday 31st of January 2012 10:31:47 AM
Old 01-31-2012
Extract text between two character positions

Greetings.

I need to extract text between two character positions, e.g: all text between character 4921 and 6534.

The text blocks are FASTA-format sequence of whole chromosomes, so basically a million A, T, G, C, combinations. E.g:
Code:
>Chr_1
ACCTGTTCAACTCTCAGGACTCTCAGGTCAACTCTCAG
CAACTCTCAGGAACTCTCAGGTCAACTCTCACTCTCAG
GTCAACTCTCCAGGAACTCTCCACTCTCAGAGGTCAAC
.......

I need to extract a region of genes, I know the character positions that are the boundaries.

I need the equivalent of what this does for lines:
Code:
sed -n 'line1,line2p" > new_file.txt

But for character positions.

Thanks!
Moderator's Comments:
Mod Comment Please use next time code tags for your code and data

Last edited by vbe; 01-31-2012 at 11:39 AM..
 

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WCWIDTH(3)						   BSD Library Functions Manual 						WCWIDTH(3)

NAME
wcwidth, wcwidth_l -- number of column positions of a wide-character code LIBRARY
Standard C Library (libc, -lc) SYNOPSIS
#include <wchar.h> int wcwidth(wchar_t wc); #include <wchar.h> #include <xlocale.h> int wcwidth_l(wchar_t wc, locale_t loc); DESCRIPTION
The wcwidth() function determines the number of column positions required to display the wide character wc. Although the wcwidth() function uses the current locale, the wcwidth_l() function may be passed a locale directly. See xlocale(3) for more information. RETURN VALUES
The wcwidth() function returns 0 if the wc argument is a null wide character (L''), -1 if wc is not printable; otherwise, it returns the number of column positions the character occupies. EXAMPLES
This code fragment reads text from standard input and breaks lines that are more than 20 column positions wide, similar to the fold(1) util- ity: wint_t ch; int column, w; column = 0; while ((ch = getwchar()) != WEOF) { w = wcwidth(ch); if (w > 0 && column + w >= 20) { putwchar(L' '); column = 0; } putwchar(ch); if (ch == L' ') column = 0; else if (w > 0) column += w; } SEE ALSO
iswprint(3), wcswidth(3), xlocale(3) STANDARDS
The wcwidth() function conforms to IEEE Std 1003.1-2001 (``POSIX.1''). BSD
August 17, 2004 BSD
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