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Top Forums Shell Programming and Scripting Extract sequences from a FASTA file based on another file Post 302881700 by bartus11 on Tuesday 31st of December 2013 10:05:44 AM
Old 12-31-2013
awk -F"[><pipe>]"split input file into fields using ">" and "<pipe>" as delimiters
'NR==FNR{execute the code that follows for the first file (File2)
sub(".$",":&",$0);insert ":" before the last character in the line ($0)
a[$0]=1}populate "a" associative array with modified line as a key
/^>/&&($2 in a){p=1}set "p" to "1" if line starts with ">" and second field can be found in "a" array
/^>/&&!($2 in a){p=0}set "p" to "0" if line starts with ">" and second field cannot be found in "a" array
p'print line if "p" is greater than "0"
File2 File1process File2 first, then File1
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PAPS(1) 						      General Commands Manual							   PAPS(1)

NAME
paps - UTF-8 to PostScript converter using Pango SYNOPSIS
paps [options] files... DESCRIPTION
paps reads a UTF-8 encoded file and generates a PostScript language rendering of the file. The rendering is done by creating outline curves through the pango ft2 backend. OPTIONS
These programs follow the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is included below. --landscape Landscape output. Default is portrait. --columns=cl Number of columns output. Default is 1. --font=desc Set the font description. Default is Monospace 12. --rtl Do rtl layout. --paper ps Choose paper size. Known paper sizes are legal, letter, a4. Default is A4. --bottom-margin=bm Set bottom margin in postscript points (1/72 inch). Default is 36. --top-margin=tm Set top margin. Default is 36. --left-margin=lm Set left margin. Default is 36. --right-margin=rm Set right margin. Default is 36. --help Show summary of options. --header Draw page header for each page. --markup Interpret the text as pango markup. --encoding=ENCODING Assume the documentation encoding is ENCODING. --lpi Set the lines per inch. This determines the line spacing. --cpi Set the characters per inch. This is an alternative method of specifying the font size. --stretch-chars Indicates that characters should be stretched in the y-direction to fill up their vertical space. This is similar to the texttops behaviour. AUTHOR
paps was written by Dov Grobgeld <dov.grobgeld@gmail.com>. This manual page was written by Lior Kaplan <kaplan@debian.org>, for the Debian project (but may be used by others). April 17, 2006 PAPS(1)
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