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Full Discussion: Grouping or appending the lines in a file through Unix
Top Forums UNIX for Dummies Questions & Answers Grouping or appending the lines in a file through Unix Post 302649011 by mkandula1983 on Wednesday 30th of May 2012 04:25:07 PM
Old 05-30-2012
Actually joeyg, I just gave a sample.. My file is something similar in these lines but is very big with lot of lines and each line having lot of info... But when i used sort command, The output was getting jumbled...

Code:
A 1 100 abc def 
A 1 100 abc def 
A 1 200 abc def 
A 1 200 xyz def 
A 1 300 abc def 
A 1 300 xyz def 
A 2 100 pqr def 
A 2 200 pqr def 
A 2 300 pqr def

But this is not what i am expecting
Last edited by Scrutinizer; 05-30-2012 at 05:32 PM.. Reason: code tags
 

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LEARN ABOUT DEBIAN

hhfilter

HHFILTER(1)							   User Commands						       HHFILTER(1)

NAME

       hhfilter - filter an alignment by maximum sequence identity of match states and minimum coverage

SYNOPSIS

       hhfilter -i infile -o outfile [options]

DESCRIPTION

       HHfilter  version  2.0.15  (June  2012)	Filter an alignment by maximum sequence identity of match states and minimum coverage (C) Johannes
       Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J.	HHblits: Lightning-fast  iterative
       protein sequence searching by HMM-HMM alignment.  Nat. Methods 9:173-175 (2011).

       -i <file>
	      read input file in A3M/A2M or FASTA format

       -o <file>
	      write to output file in A3M format

       -a <file>
	      append to output file in A3M format

OPTIONS

       -v <int>
	      verbose mode: 0:no screen output	1:only warings	2: verbose

       -id    [0,100]  maximum pairwise sequence identity (%) (def=90)

       -diff [0,inf[
	      filter MSA by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50 (def=0)

       -cov   [0,100]  minimum coverage with query (%) (def=0)

       -qid   [0,100]  minimum sequence identity with query (%) (def=0)

       -qsc   [0,100]  minimum score per column with query  (def=-20.0)

       -neff [1,inf]
	      target diversity of alignment (default=off)

   Input alignment format:
       -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted)

       -M first
	      use FASTA: columns with residue in 1st sequence are match states

       -M [0,100]
	      use FASTA: columns with fewer than X% gaps are match states

       Example: hhfilter -id 50 -i d1mvfd_.a2m -o d1mvfd_.fil.a2m

hhfilter 2.0.15 						     June 2012							       HHFILTER(1)
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