NAME

uniprotdata2fasta.pl

DESCRIPTION

Read a uniprot .dat (sprot, trembl...) and convert it into a fasta file, expanding VAR_SPLIC, CHAIN, PEPT annotations.

FT annotation, such as MOD_RES, VARIANT... are kept in the fasta header coherently with the sequence modifictaion

SYNOPSIS

uniprotdata2fasta.pl --in=uniprot_sprot.dat --out=uniprot_sprot.fasta

ARGUMENTS

--in=file

A .dat file [default is stdin]

-out=file

A .fasta file [default is stdout]

OPTIONS

--noderived

does not produce the derived sequences (VAR_SEQ, CHAIN...)

--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

Alexandre Masselot, www.genebio.com