—package
MS::Reader::MzIdentML::Peptide;
use
strict;
use
warnings;
sub
id {
return
$_
[0]->{id} }
sub
seq {
return
$_
[0]->{PeptideSequence}->{pcdata} }
sub
mods {
return
$_
[0]->{Modification} }
1;
__END__
=pod
=encoding UTF-8
=head1 NAME
MS::Reader::MzIdentML::Peptide - mzIdentML peptide object
=head1 SYNOPSIS
my $pep = $search->fetch_peptide_by_id('PEP_1');
say $pep->id;
say $pep->seq;
for (@{ $pep->mods }) {
say $_->{monoisotopicMassDelta};
}
=head1 DESCRIPTION
The C<MS::Reader::MzIdentML::Peptide> class represents a <Peptide> element in
the search results. This is a specific peptide isoform with known sequence and
modifications, and can be referenced elsewhere in the results.
=head1 METHODS
=head2 id
my $id = $pep->id;
Returns the peptide ID, which is a unique identifier within the results file
=head2 seq
my $seq = $pep->seq;
Returns the peptide sequence as a one-letter IUPAC string
=head2 mods
my $mods = $pep->mods;
Returns a reference to an array of modifications, each of which is a nested
hash structure. The details of this structure are currently undocumented and
need to be deduced using C<Data::Dumper> to be utilized. At some point a
Modification class will be implemented to make utilization of this data
easier.
=head1 CAVEATS AND BUGS
The API is in alpha stage and is not guaranteed to be stable.
Please reports bugs or feature requests through the issue tracker at
=head1 AUTHOR
Jeremy Volkening <jdv@base2bio.com>
=head1 COPYRIGHT AND LICENSE
Copyright 2015-2019 Jeremy Volkening
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program 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 General Public License for more
details.
You should have received a copy of the GNU General Public License along with
this program. If not, see <http://www.gnu.org/licenses/>.
=cut