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Top Forums UNIX for Beginners Questions & Answers Match patterns between two files and extract certain range of strings Post 303041964 by vgersh99 on Monday 9th of December 2019 11:44:45 AM
Old 12-09-2019
a bit verbose, but a possible starter.
awk -f bunny.awk inputfile2.txt inputfile1.fa where bunny.awk is:
Code:
function printRec() {
   #print a[f], s[f], e[f]
   for ( i in s) {
      split(i,t, OFS)
      if (f == ">" t[1])
        print ">" i ORS substr(a[f],s[i],e[i]-s[i]+1)
   }
   f=""
   split("",a)
}
FNR==NR {
   idx=$1 OFS $2 OFS $3
   s[idx]=$2
   e[idx]=$3
   next
}
/>/ && f {
   printRec()
}
f { a[f]=(f in a)?a[f] $1:$1 }
/^>/ { f=$1 }
END { printRec() }

results in:
Code:
>l-WR24-1:1 1 71
GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGGGGCGGAGGGCG
>l-ZF385A-2:1 33 105
TGAGCTTCGGGTCACCGCCCCTCCAGAGGCTGAGTACTCAGGACTCGTCAGACACCCAGGGGTGAGATGAGAC
>l-YJC-1:1 1 161
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCA
>l-YJC-1:1 1 165
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCAGGCA


Last edited by vgersh99; 12-09-2019 at 12:51 PM..
This User Gave Thanks to vgersh99 For This Post:
 

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file-roller(1)							   User Commands						    file-roller(1)

NAME
file-roller - create, view, modify, or unpack an archive SYNOPSIS
file-roller [--add] [--add-to=archive] [--default-dir=folder] [--extract] [--extract-here] [--extract-to=folder] [--force] [gnome-std- options] DESCRIPTION
The File Roller application enables you to create, view, modify, or unpack an archive. An archive is a file that acts as a container for other files. An archive can contain many files, folders, and subfolders, usually in compressed form. OPTIONS
The following options are supported: -d, --add Ask for the name of the archive, then add the files, then quit the application. -a, --add-to=archive Add files to the specified archive, then quit the application. --default-dir=folder Specify the default folder for the --add and --extract options. -f, --extract Ask for the name of the destination folder, then extract the files, then quit the application. -h, --extract-here Extract archives using the archive name as destination folder and quit the program. -e, --extract-to=folder Extract archives to the specified folder, then quit the application. --force Create the destination folder without asking for confirmation. gnome-std-options Standard options available for use with most GNOME applications. See gnome-std-options(5) for more infor- mation. EXAMPLES
Example 1: Unpacking an Archive example% file-roller --extract archive EXIT STATUS
The following exit values are returned: 0 Application exited successfully >0 Application exited with failure FILES
The following files are used by this application: /usr/bin/file-roller Executable for File Roller application. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNW | +-----------------------------+-----------------------------+ |Interface stability |Volatile | +-----------------------------+-----------------------------+ SEE ALSO
File Roller Manual ar(1), tar(1), unzip(1), zip(1), attributes(5), gnome-std-options(5) NOTES
Written by Laszlo Kovacs, Sun Microsystems Inc., 2003, 2004, 2007. SunOS 5.11 08 Nov 2007 file-roller(1)
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