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Top Forums Shell Programming and Scripting How to remove those sequence with same amino acid?What command line I should type? Post 302278432 by koti_rama on Tuesday 20th of January 2009 08:07:06 AM
Old 01-20-2009
try like this:
s1-> this contains you source date
out-> out put file


while read line
do
acid=`echo $line | awk ' FS=" " {print $1}'`
count=`grep $acid s1 | wc -l`
if [ "$count" -gt "1" ]; then
echo " Acid $acid exit in out file"
continue;
else
echo "$line" >>out.log
fi
done<s1

Last edited by koti_rama; 01-20-2009 at 09:16 AM..
 

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BP_AACOMP(1p)						User Contributed Perl Documentation					     BP_AACOMP(1p)

NAME
aacomp - amino acid composition of protein sequences SYNOPSIS
aacomp [-f/--format FORMAT] [-h/--help] filename or aacomp [-f/--format FORMAT] < filename or aacomp [-f/--format FORMAT] -i filename DESCRIPTION
This scripts prints out the count of amino acids over all protein sequences from the input file. OPTIONS
The default sequence format is fasta. The sequence input can be provided using any of the three methods: unnamed argument aacomp filename named argument aacomp -i filename standard input aacomp < filename FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason@bioperl.org HISTORY
Based on aacomp.c from an old version of EMBOSS perl v5.14.2 2012-03-02 BP_AACOMP(1p)
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