Alexandre Masselot > InSilicoSpectro-Databanks > ncbinr2phenyxfasta.pl

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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

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