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MS-0.207003
River stage zero No dependents
++
/ MS::Reader::MzIdentML::PeptideEvidence

NAME

MS::Reader::MzIdentML::PeptideEvidence - mzIdentML peptide evidence object

SYNOPSIS

    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;

DESCRIPTION

The 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.

METHODS

id

    my $id = $pe->id;

Returns the peptide evidence ID, which is a unique identifier within the results file

peptide_id

    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 MS::Reader::MzIdentML::Peptide object.

search_db

    my $db_id = $pe->search_db;

Returns the ID of the search database the evidence comes from.

start

end

pre

post

    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.

frame

    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.

is_decoy

    next if ($pe->is_decoy);

Returns a boolean value indicating whether the peptide evidence is from a decoy protein.

trl_table

    my $tbl_id = $pe->trl_table;

Returns the ID of the translation table associated with the peptide evidence.

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 https://github.com/jvolkening/p5-MS/issues.

AUTHOR

Jeremy Volkening <jdv@base2bio.com>

COPYRIGHT AND LICENSE

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/>.