Scroll to navigation

Bio::DB::HTS::Query(3pm) User Contributed Perl Documentation Bio::DB::HTS::Query(3pm)

LICENSE

Copyright [2015-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

AUTHOR

Rishi Nag <rishi@ebi.ac.uk<gt>

NAME

Bio::DB::HTS::Query -- Object representing the query portion of a BAM/SAM alignment

SYNOPSIS

Given an alignment retrieved from a Bio::DB::HTS database,

 my $query = $alignment->query;
 my $name   = $query->display_name;
 my $start  = $query->start;
 my $end    = $query->end;
 my $dna    = $query->dna;    # dna string
 my $seq    = $query->seq;    # Bio::PrimarySeq object
 my @scores = $query->qscore; # quality score

DESCRIPTION

This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment.

Methods

$seqid = $query->seq_id
The name of the read.
$name = $query->name
The read name (same as seq_id in this case).
$name = $query->display_name
The read display_name (same as seq_id in this case).
$tag = $query->primary_tag
The string "match".
$tag = $query->source_tag
The string "sam/bam".
$start = $query->start
The start of the match in read coordinates.
$end = $query->end
The end of the match in read coordinates;
$len = $query->length
The length of the read.
$seq = $query->seq
A Bio::PrimarySeq representing the read sequence in REFERENCE orientation.
$scores = $query->qscore
The read quality scores. In a list context, a list of integers equal in length to the read sequence length. In a scalar context, an array ref. The qscores are in REFERENCE sequence orientation.
$dna = $query->dna
The DNA string in reference sequence orientation.
$strand = $query->strand
If the query was reversed to align it, -1. Otherwise +1.
$seq = $query->subseq($start,$end)
Return a Bio::PrimarySeq object representing the requested subsequence on the read.

SEE ALSO

Bio::Perl, Bio::DB::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants

2024-10-31 perl v5.40.0