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Top Forums UNIX for Beginners Questions & Answers How to count the length of fasta sequences? Post 303033626 by RavinderSingh13 on Tuesday 9th of April 2019 09:24:20 AM
Old 04-09-2019
Quote:
Originally Posted by dineshkumarsrk
Thank you singh,
Your command prints all the sequences. However, I need to print only few sequences length as listed in id.txt file. If I did not understand your commands properly, please let me know, where to include id.txt file in your command?
Oh ok, I was in impression that you want to print all seq strings length in a single Input_file, could you please try following now.
Code:
awk 'FNR==NR{a[$0];next} /^>/ && sub(/^>/,""){;found=val="";if($0 in a){val=$0;found=1};next} found{print val,length($0)} ' ids.txt  Input_file

Output will be as follows.
Code:
seq1 6
seq2 7

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
 

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GAPPLETVIEWER(1)                                                        GNU                                                       GAPPLETVIEWER(1)

NAME
gappletviewer - Load and runs an applet SYNOPSIS
appletviewer [OPTION]... URL... appletviewer [OPTION]... -code CODE appletviewer [OPTION]... -plugin INPUT,OUTPUT DESCRIPTION
The appletviewer tool loads and runs an applet. Use the first form to test applets specified by tag. The URL should resolve to an HTML document from which the appletviewer will extract applet tags. The APPLET, EMBED and OBJECT tags are supported. If a given document contains multiple applet tags, all the applets will be loaded, with each applet appearing in its own window. Likewise, when multiple URLs are specified, each applet tag instance is given its own window. If a given document contains no recognized tags the appletviewer does nothing. appletviewer http://www.gnu.org/software/classpath/ Use the second form to test an applet in development. This form allows applet tag attributes to be supplied on the command line. Only one applet may be specified using the -code option. The -code option overrides the URL form -- any URLs specified will be ignored. appletviewer -code Test.class -param datafile,data.txt gcjwebplugin uses the third form to communicate with the appletviewer through named pipes. OPTIONS
URL OPTIONS -debug This option is not yet implemented but is provided for compatibility. -encoding CHARSET Use this option to specify an alternate character encoding for the specified HTML page. APPLET TAG OPTIONS -code CODE Use the -code option to specify the value of the applet tag CODE attribute. -codebase CODEBASE Use the -codebase option to specify the value of the applet tag CODEBASE attribute. -archive ARCHIVE Use the -archive option to specify the value of the applet tag ARCHIVE attribute. -width WIDTH Use the -width option to specify the value of the applet tag WIDTH attribute. -height HEIGHT Use the -height option to specify the value of the applet tag HEIGHT attribute. -param NAME,VALUE Use the -param option to specify values for the NAME and VALUE attributes of an applet PARAM tag. PLUGIN OPTION -plugin INPUT,OUTPUT gcjwebplugin uses the -plugin option to specify the named pipe the appletviewer should use for receiving commands (INPUT) and the one it should use for sending commands to gcjwebplugin (OUTPUT). DEBUGGING OPTION -verbose Use the -verbose option to have the appletviewer print debugging messages. STANDARD OPTIONS -help Use the -help option to have the appletviewer print a usage message, then exit. -version Use the -version option to have the appletviewer print its version, then exit. -JOPTION Use the -J option to pass OPTION to the virtual machine that will run the appletviewer. Unlike other options, there must not be a space between the -J and OPTION. BUGS
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0.98 2010-07-05 GAPPLETVIEWER(1)
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