- CAVEATS AND BUGS
- COPYRIGHT AND LICENSE
MS::Reader::MzIdentML::PeptideEvidence - mzIdentML peptide evidence object
my $pe = $search->fetch_peptideevidence_by_id($EV_ID); say $pe->id; say $pe->start; say $pe->end; say $pe->pre; say $pe->post; say $pe->frame; my $pep_id = $pe->peptide_id; my $db_id = $pe->search_db; my $is_decoy = $pe->is_decoy; my $tbl_id = $pe->trl_table;
MS::Reader::MzIdentML::PeptideEvidence class represents a <PeptideEvidence> element in the search results. This links peptide sequences to their location in a database protein, as well as including other information such as decoy status.
my $id = $pe->id;
Returns the peptide evidence ID, which is a unique identifier within the results file
my $pep_id = $pe->peptide_id; my $pep = $search->fetch_peptide_by_id( $pep_id );
Returns the ID of the associated Peptide element, which can be used to look up a corresponding
my $db_id = $pe->search_db;
Returns the ID of the search database the evidence comes from.
my $start_loc = $pe->start; my $end_loc = $pe->end; my $prev_aa = $pe->pre; my $next_aa = $pe->post;
Return information related to a peptide's context within it's parent protein: start coordinate, end coordinate, previous amino acid, and subsequent amino acid. None of these values are guaranteed to be defined.
my $reading_frame = $pe->frame;
The translation frame of the peptide, in the range of -3 to -1 or 1 to 3. Not guaranteed to be defined.
next if ($pe->is_decoy);
Returns a boolean value indicating whether the peptide evidence is from a decoy protein.
my $tbl_id = $pe->trl_table;
Returns the ID of the translation table associated with the peptide evidence.
The API is in alpha stage and is not guaranteed to be stable.
Please reports bugs or feature requests through the issue tracker at https://github.com/jvolkening/p5-MS/issues.
Jeremy Volkening <email@example.com>
Copyright 2015-2016 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/>.