mor::Acquisition - Genbank downloader
use DBI;
use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;
use Bio::SeqIO;
use mor::Log;
use mor::Settings;
use mor::DatabaseIO;
use mor::Utilities;
use mor::Acquisition;
This package deals with querying GenBank for (new) sequences matching the query string and saving the data for later processing.
Title : queryGB
Usage : my @sequences = mor::Acquisition::queryGB($table, $saveFile, $queryString, $mindate, $maxdate)
Function: Downloads the sequences using $queryString that were deposited in genbank between
the dates: $mindate and $maxdate. It then saves the files to $table in a mysql database
and to the file $saveFile. It returns an array of the sequences for further processing.
Returns : An array of Bio::Seq::RichSeq objects.
Args : name of the table for the sequences to be stored
name of the file that the sequences will be saved to
genbank query string
earliest date to retrieve from genbank
latest date to retrieve from genbank
Title : tryQueryGB
Usage : my @seqs = mor::Acquisition::tryQueryGB($mindate,$maxdate,$queryString,$table,$answer)
Function: Acts as a wrapper around the queryGB function, allows for the program to
choose between the previous downloaded file or to download more sequences
from genbank to be saved to the database
Returns : An array of Bio::Seq::RichSeq objects.
Args : name of the table for the sequences to be stored
name of the file that the sequences will be saved to
genbank query string
earliest date to retrieve from genbank
latest date to retrieve from genbank
'u' or 'i' for (u)se the file or (i)gnore the file and download from genbank.
The mor Team - http://mor.clarku.edu/morTeam.php