Bio::DB::Sam 1.33

Bio::DB::Sam is a module that provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application.

SYNOPSIS

 use Bio::DB::Sam;

 # high level API
 my $sam = Bio::DB::Sam->new(-bam =>"data/ex1.bam",
 -fasta=>"data/ex1.fa",
 );

 my @targets = $sam->seq_ids;
 my @alignments = $sam->get_features_by_location(-seq_id => 'seq2',
 -start => 500,
 -end => 800);
 for my $a (@alignments) {
 my $seqid = $a->seq_id;
 my $start = $a->start;
 my $end = $a->end;
 my $strand = $a->strand;
 my $cigar = $a->cigar_str;
 my $paired = $a->get_tag_values('PAIRED');
 my $ref_dna = $a->dna; # reference sequence
 my $query_dna = $a->query->dna; # query sequence
 my @scores = $a->qscore; # per-base quality scores
 my $match_qual= $a->qual; # quality of the match
 }

 my @pairs = $sam->get_features_by_location(-type => 'read_pair',
 -seq_id => 'seq2',
 -start => 500,
 -end => 800);

 for my $pair (@pairs) {
 my $length = $pair->length; # insert length
 my ($first_mate,$second_mate) = $pair->get_SeqFeatures;
 my $f_start = $first_mate->start;
 my $s_start = $second_mate->start;
 }

 # low level API
 my $bam = Bio::DB::Bam->open('/path/to/bamfile');
 my $header = $bam->header;
 my $target_count = $header->n_targets;
 my $target_names = $header->target_name;
 while (my $align = $bam->read1) {
 my $seqid = $target_names->[$align->tid];
 my $start = $align->pos+1;
 my $end = $align->calend;
 my $cigar = $align->cigar_str;
 }

 my $index = Bio::DB::Bam->index_open('/path/to/bamfile');
 my $callback = sub {
 my $alignment = shift;
 my $start = $alignment->start;
 my $end = $alignment->end;
 my $seqid = $target_names->[$alignment->tid];
 print $alignment->qname," aligns to $seqid:$start..$end
";
 }
 my $header = $index->header;
 $index->fetch($bam,$header->parse_region('seq2'),$callback);


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Requirements:

· Perl