NAME
ncbinr2phenyxfasta.pl - tranfoorm ncbirn bank into fasta with annotated headers
DESCRIPTION
SYNOPSIS
ncbinr2phenyxfasta.pl --in=EST_others.fasta --out=/tmp/est_others.fasta --defaulttaxid=1 --taxo=/tmp/gi_taxid_nucl.dmp --sorted --norewind
ARGUMENTS
--in=infile.fasta
An input fasta file
--taxo=file
--out=outfile.fasta
A .fasta file [default is stdout]
OPTIONS
--sorted
The entries both in fasta and taxo file are sorted (there can be (few) miss sorting in the taxonomy file)
--defaulttaxid=int
A taxonomy to batttribute to entries where there is nor registrated taxonomy
--norewind
Disallow rewind of taxonomy file when a taxid is missing
--help
--man
--verbose
Setting an environment vartiable DO_NOT_DELETE_TEMP=1 will keep the temporay file after the script exit
EXAMPLE
COPYRIGHT
Copyright (C) 2004-2006 Geneva Bioinformatics www.genebio.com
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
AUTHORS
Djibril Ousmanou,
Alexandre Masselot, www.genebio.com