Bio::Index::Fasta - Interface for indexing (multiple) fasta files
# Complete code for making an index for several # fasta files use Bio::Index::Fasta; my $Index_File_Name = shift; my $inx = Bio::Index::Fasta->new( -filename => $Index_File_Name, -write_flag => 1); $inx->make_index(@ARGV); # Print out several sequences present in the index # in Fasta format use Bio::Index::Fasta; my $Index_File_Name = shift; my $inx = Bio::Index::Fasta->new($Index_File_Name); my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object $out->write_seq($seq); } # or, alternatively my $seq = $inx->get_Seq_by_id($id); #identical to fetch
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fasta files, and retrieving the sequence from them.
Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used a a Sequence database for other parts of bioperl
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : _initialize Usage : $index->_initialize Function: Calls $index->SUPER::_initialize(), and then adds the default id parser for fasta files. Example : Returns : Args :
Title : _file_format Function: The file format for this package, which is needed by the SeqIO system when reading the sequence. Returns : 'Fasta'
Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index FASTA format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args :
Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Useful for (for instance) specifying a different parser for different flavours of FASTA file. Returns \&default_id_parser (see below) if not set. If you supply your own id_parser subroutine, then it should expect a fasta description line. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : ref to CODE if called without arguments Args : CODE
Title : default_id_parser Usage : $id = default_id_parser( $header ) Function: The default Fasta ID parser for Fasta.pm Returns $1 from applying the regexp /^>\s*(\S+)/ to $header. Returns : ID string Args : a fasta header line string
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.