--- name: "Bio::DB::Fasta" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::DB::Fasta" --- # Bio::DB::Fasta(3pm) Fast indexed access to fasta files ## NAME Bio::DB::Fasta - Fast indexed access to fasta files ## SYNOPSIS ``` use Bio::DB::Fasta; # Create database from a directory of Fasta files my $db = Bio::DB::Fasta->new('/path/to/fasta/files/'); my @ids = $db->get_all_primary_ids; # Simple access my $seqstr = $db->seq('CHROMOSOME_I', 4_000_000 => 4_100_000); my $revseq = $db->seq('CHROMOSOME_I', 4_100_000 => 4_000_000); my $length = $db->length('CHROMOSOME_I'); my $header = $db->header('CHROMOSOME_I'); my $alphabet = $db->alphabet('CHROMOSOME_I'); # Access to sequence objects. See Bio::PrimarySeqI. my $seq = $db->get_Seq_by_id('CHROMOSOME_I'); my $seqstr = $seq->seq; my $subseq = $seq->subseq(4_000_000 => 4_100_000); my $trunc = $seq->trunc(4_000_000 => 4_100_000); my $length = $seq->length; # Loop through sequence objects my $stream = $db->get_PrimarySeq_stream; while (my $seq = $stream->next_seq) { # Bio::PrimarySeqI stuff } # Filehandle access my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files/'); while (my $seq = <$fh>) { # Bio::PrimarySeqI stuff } # Tied hash access tie %sequences,'Bio::DB::Fasta','/path/to/fasta/files/'; print $sequences{'CHROMOSOME_I:1,20000'}; ``` ## DESCRIPTION Bio::DB::Fasta provides indexed access to a single Fasta file, several files, or a directory of files. It provides persistent random access to each sequence entry (either as a Bio::PrimarySeqI-compliant object or a string), and to subsequences within each entry, allowing you to retrieve portions of very large sequences without bringing the entire sequence into memory. Bio::DB::Fasta is based on Bio::DB::IndexedBase. See this module's documentation for details. The Fasta files may contain any combination of nucleotide and protein sequences; during indexing the module guesses the molecular type. Entries may have any line length up to 65,536 characters, and different line lengths are allowed in the same file. However, within a sequence entry, all lines must be the same length except for the last. An error will be thrown if this is not the case. The module uses /^\>(\\S+)/ to extract the primary ID of each sequence from the Fasta header. See -makeid in Bio::DB::IndexedBase to pass a callback routine to reversibly modify this primary ID, e.g. if you wish to extract a specific portion of the gi\|gb\|abc\|xyz GenBank IDs. ## DATABASE CREATION AND INDEXING The object-oriented constructor is **new()**, the filehandle constructor is **newFh()** and the tied hash constructor is **tie()**. They all allow one to index a single Fasta file, several files, or a directory of files. See Bio::DB::IndexedBase. ## SEE ALSO Bio::DB::IndexedBase Bio::DB::Qual Bio::PrimarySeqI ## AUTHOR Lincoln Stein \. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ For BioPerl-style access, the following methods are provided: ### get\_Seq\_by\_id ``` Title : get_Seq_by_id, get_Seq_by_acc, get_Seq_by_primary_id Usage : my $seq = $db->get_Seq_by_id($id); Function: Given an ID, fetch the corresponding sequence from the database. Returns : A Bio::PrimarySeq::Fasta object (Bio::PrimarySeqI compliant) Note that to save resource, Bio::PrimarySeq::Fasta sequence objects only load the sequence string into memory when requested using seq(). See L for methods provided by the sequence objects returned from get_Seq_by_id() and get_PrimarySeq_stream(). Args : ID ``` ### get\_PrimarySeq\_stream ``` Title : get_PrimarySeq_stream Usage : my $stream = $db->get_PrimarySeq_stream(); Function: Get a stream of Bio::PrimarySeq::Fasta objects. The stream supports a single method, next_seq(). Each call to next_seq() returns a new Bio::PrimarySeq::Fasta sequence object, until no more sequences remain. Returns : A Bio::DB::Indexed::Stream object Args : None ``` ## For simple access, the following methods are provided: ### new ``` Title : new Usage : my $db = Bio::DB::Fasta->new( $path, %options); Function: Initialize a new database object. When indexing a directory, files ending in .fa,fasta,fast,dna,fna,faa,fsa are indexed by default. Returns : A new Bio::DB::Fasta object. Args : A single file, or path to dir, or arrayref of files Optional arguments: see Bio::DB::IndexedBase ``` ### seq ``` Title : seq, sequence, subseq Usage : # Entire sequence string my $seqstr = $db->seq($id); # Subsequence my $subseqstr = $db->seq($id, $start, $stop, $strand); # or... my $subseqstr = $db->seq($compound_id); Function: Get a subseq of a sequence from the database. For your convenience, the sequence to extract can be specified with any of the following compound IDs: $db->seq("$id:$start,$stop") $db->seq("$id:$start..$stop") $db->seq("$id:$start-$stop") $db->seq("$id:$start,$stop/$strand") $db->seq("$id:$start..$stop/$strand") $db->seq("$id:$start-$stop/$strand") $db->seq("$id/$strand") In the case of DNA or RNA sequence, if $stop is less than $start, then the reverse complement of the sequence is returned. Avoid using it if possible since this goes against Bio::Seq conventions. Returns : A string Args : ID of sequence to retrieve or Compound ID of subsequence to fetch or ID, optional start (defaults to 1), optional end (defaults to length of sequence) and optional strand (defaults to 1). ``` ### length ``` Title : length Usage : my $length = $qualdb->length($id); Function: Get the number of residues in the indicated sequence. Returns : Number Args : ID of entry ``` ### header ``` Title : header Usage : my $header = $db->header($id); Function: Get the header line (ID and description fields) of the specified sequence. Returns : String Args : ID of sequence ``` ### alphabet ``` Title : alphabet Usage : my $alphabet = $db->alphabet($id); Function: Get the molecular type of the indicated sequence: dna, rna or protein Returns : String Args : ID of sequence ```