Bio::DB::GenPept - Database object interface to GenPept
$gb = new Bio::DB::GenPept; $seq = $gb->get_Seq_by_id('195055'); # Unique ID # or ... $seq = $gb->get_Seq_by_acc('195055'); # Accession Number
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept database at NCBI, via an Entrez query.
WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Batch Entrez support will likely be supported in a future version of DB::GenPept.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id($uid); Function: Gets a Bio::Seq object by its unique identifier/name Returns : a Bio::Seq object Args : $uid : the id (as a string) of the desired sequence entry
Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a Bio::Seq object by its accession number Returns : a Bio::Seq object Args : $acc : the accession number of the desired sequence entry Note : For GenPept, this just calls the same code for get_Seq_by_id()
Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries
Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenPept, this just calls the same code for get_Stream_by_id()
Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique id's/accession numbers.
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.