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Full Discussion: Sequence extraction
Top Forums Shell Programming and Scripting Sequence extraction Post 302951309 by Scrutinizer on Wednesday 5th of August 2015 03:39:48 AM
Old 08-05-2015
Maybe because FS is set to '\t' and there appear to be no TABs in your second sample file, so the fields will not match. And you are setting the index to the entire record, save the first character. which is probably not what you want (you probably meant to use $1 here, but that would not be a sure way to do it either, because in the FASTA format the identifier is allowed to contain spaces). And the FASTA file is word wrapped, so you need to take out the newlines and not use getline to get only the second line ....

The best way to do that is is to use ">" as a record separator and use "\n" as the field separator. By setting OFS as the empty string, and assigning a value to one of the fields, all newlines will be replaced by empty strings, so this will effectively remove the word wrap. And the sequence will become one continuous string, which will make it suitable for substring selection.

Using your file order, we would get something like this.
Code:
awk 'NR==FNR{i=$1; $1=x; A[i]=$0; next} $1 in A{print ">" $1 ORS substr(A[$1], $2, $3-$2+1)}' RS=\> FS='\n' OFS= file1 FS=" " RS="\n" file2


If we read the files the other way around, then it becomes more memory efficient:
Code:
awk 'NR==FNR{S[$1]=$2; E[$1]=$3; next} $1 in S{i=$1; $1=x; print RS i FS substr($0,S[i],E[i]-S[i]+1)}' file2 RS=\> FS='\n' OFS= file1


Last edited by Scrutinizer; 08-05-2015 at 04:52 AM..
 

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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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