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Full Discussion: Changing from FASTA to PHYLIP format
Top Forums Shell Programming and Scripting Changing from FASTA to PHYLIP format Post 302499225 by Xterra on Wednesday 23rd of February 2011 05:35:10 PM
Old 02-23-2011
I need to combine both codes
Code:
awk '$1=substr($1"       ",1,8)"  "' FS="\n" OFS= RS=\> file

Code:
awk '{s=length($2)}END{print NR-1, s}' file

So I can get the desired output
Code:
3 100 
SeID1_____AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGACTGACAGGTTCAAAGGCTGCAGTGCAGTGACGTGACGATTT 
Sequence__AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGACTGACAGGTTCAAAGGCTGCAGTGCAGTGACGTGACGATTT 
Seq-39____AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGACTGACAGGTTCAAAGGCTGCAGTGCAGTGACGTGACGATTT

I have been trying but I just cannot get the code to do what I want.
Can anyone explain me how can I combine them?
Thanks!
Last edited by Xterra; 02-23-2011 at 06:59 PM..
 

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LEARN ABOUT DEBIAN

fastautils

fastautils(1)					     FASTA format file manipulation utilities					     fastautils(1)

NAME

       fastautils - FASTA format file manipulation utilities

SYNOPSIS

       fastachecksum [ options ] <input file>

       fastaclean

       fastaclip

       fastacomposition

       fastadiff

       fastaexplode

       fastafetch

       fastahardmask

       fastaindex

       fastalength

       fastanrdb

       fastaoverlap

       fastareformat

       fastaremove

       fastarevcomp

       fastasoftmask

       fastasort

       fastasplit

       fastasubseq

       fastatranslate

       fastavalidcds

DESCRIPTION

       These  are  utilities  for  the manipulation of FASTA format sequence databases which are distributed with the exonerate sequence alignment
       program.

ENVIRONMENT

       Not documented yet.

EXAMPLES

       fastalength sequence.fasta
	      blah blah

VERSION

       This documentation accompanies version 2.2.0 of the exonerate package.

AUTHOR

       Guy St.C. Slater.  <guy@ebi.ac.uk>.  See the AUTHORS file accompanying the source code for a list of contributors.

AVAILABILITY

       This source code for the exonerate package is available under the terms of the GNU general public licence.

       Please see the file COPYING which was distrubuted with this package, or http://www.gnu.org/licenses/gpl.txt for details.

       This package has been developed as part of the ensembl project.	Please see http://www.ensembl.org/ for more information.

SEE ALSO

       exonerate(1),e-PCR

fastautils							    March 2003							     fastautils(1)
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