NAME
InSilico::Databanks::DBEntry - fasta databank entry + header's annotated info
SYNOPSIS
DESCRIPTION
describes an databnk entry (header + sequence)
FUNCTIONS
METHODS
my $dbe=InSilico::Databanks::DBEntry->new([\%h]);
Accessors/Setters
$dbe->AC([val])
get/set accession code
$dbe->ID([val])
get/set accession ID
$dbe->dbName([val])
[GS]et databank name
$dbe->taxoID([val])
[GS]et taxonomy if (typically NCBI taxid
$dbe->description([val])
$dbe->sequence([val])
Get/Set AC, ID, ...
$dbe->seqType(["AA"|"DNA"])
Get or set the sequence type
$dbe->annotatedModRes(string|[[pos1, mod1], [pos2, mod2]]);
get or set annotated PTM from a string (e.g. (1|ACET_nterm)(2|ACET_nterm)(185|PHOS)) or an array. All previously set TPM are removed
$dbe->add_annotatedModRes(pos, modkey)
add an annotated PTM
$dbe->clear_annotatedModRes()
remove all annotated modres
$dbe->variants(string|[[pos1, seq1a, seq1b], [pos2, seq2a, seq2b]]);
get or set variant a string (e.g. ("(9|F|Y)(30|D|N)(41|A|G)(43|Q|R)") or an array. All previously set TPM are removed
$dbe->add_variant(pos, seqa, seqb)
add a VARIANT, replacing seqa by seqb (often just one aminoacid) at pos
$dbe->clear_variants()
remove all Variants
I/O
$dbe->readFasta($fastacontent);
read info from fasta contents (fitrs line with '>' and info + remaining is sequence.
$dbe->printFasta();
print the entry under fasta format (use SelectSaver or whatever select method to redirect towards a file descriptor);
$dbe->printHtml();
Print the entry under a html format.
EXAMPLES
SEE ALSO
COPYRIGHT
Copyright (C) 2004-2005 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