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Full Discussion: Sequence extraction
Top Forums Shell Programming and Scripting Sequence extraction Post 302951305 by harpreetmanku04 on Wednesday 5th of August 2015 02:28:34 AM
Old 08-05-2015
Sequence extraction

i want to extract specific region of interest from big file. i have only start position, end position and seq id, see my query is:

I have file1 is this

Code:
>GL3482.1
GAACTTGAGATCCGGGGA
GCAGTGGATCTCCACCAG
CGGCCAGAACTGGTGCAC
CTCCAGGCCAGCCTCGTC
CTGCGTGTC
>GL3550.1
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>GL3472.1
TTTTCCTGTTCACTGCTGCTTTTCTATAGACAGCA
GCAGCAAGCAGTAAGAGAAAGTA


file2 is this :

Code:
seq id     start    end
GL3482.1   323100   323743
GL3550.1   41911    40888
GL3472.1   274408   272617

and i want result like this:

Code:
>GL3482.1 
TTGAGA
>GL3550.1 
GGCATTTTTGTG
>GL3472.1
TTCCTGTT

when i run this command :

Code:
$ awk 'NR==FNR{if($0~/^>/){i=substr($0,2);getline};a[i]=a[i] $0;next}{print ">" $1 ORS substr(a[$1], $2, $3-$2+1)}' file1 FS=\\t file2

i got no output or output file. why so?
Moderator's Comments:
Mod Comment Please use CODE tags as required by the forum rules you agreed to when you joined this forum.


---------- Post updated at 01:28 AM ---------- Previous update was at 01:21 AM ----------

i am using Ubuntu OS

Last edited by Scrutinizer; 08-05-2015 at 04:07 AM.. Reason: Add CODE tags, remove extraneous closing COLOR tag. Removed spurious space and a newline from first sample file
 

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curs_scroll(3X) 														   curs_scroll(3X)

NAME
scroll, scrl, wscrl - scroll a curses window SYNOPSIS
#include <curses.h> int scroll(WINDOW *win); int scrl(int n); int wscrl(WINDOW *win, int n); DESCRIPTION
The scroll routine scrolls the window up one line. This involves moving the lines in the window data structure. As an optimization, if the scrolling region of the window is the entire screen, the physical screen may be scrolled at the same time. For positive n, the scrl and wscrl routines scroll the window up n lines (line i+n becomes i); otherwise scroll the window down n lines. This involves moving the lines in the window character image structure. The current cursor position is not changed. For these functions to work, scrolling must be enabled via scrollok. RETURN VALUE
These routines return ERR upon failure, and OK (SVr4 only specifies "an integer value other than ERR") upon successful completion. NOTES
Note that scrl and scroll may be macros. The SVr4 documentation says that the optimization of physically scrolling immediately if the scroll region is the entire screen "is" per- formed, not "may be" performed. This implementation deliberately does not guarantee that this will occur, to leave open the possibility of smarter optimization of multiple scroll actions on the next update. Neither the SVr4 nor the XSI documentation specify whether the current attribute or current color-pair of blanks generated by the scroll function is zeroed. Under this implementation it is. PORTABILITY
The XSI Curses standard, Issue 4 describes these functions. SEE ALSO
curses(3X), curs_outopts(3X) curs_scroll(3X)
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