GitLab

Split source table into 2; one for "high level" source name and the other (source_url) to contain the list of actual files we download from.

Added UNIQUE constraint for accession & source to xref table.

Beginning of a parser for RefSeq xrefs. Just creates xrefs and primary xref for protein RefSeq files - still need to parse and somehow incorporate mRNA files

Allowed for file extensions when guessing source ID from file name.

documentation of fetch_by_region-method fixed

WAS :         $slice = $sa->fetch_by_region('x', 100000, 200000);
CHANGED TO :  $slice = $sa->fetch_by_region('chromosome','x', 100000, 200000);

Modified INSERTs for source table to not have hard-coded source_id.

Started adding sources for RefSeq files.

Incorporated harvesting functionality; automatically call appropriate parser after file has been downloaded. Changes to SwissProtParser to allow it to be run from the command-line or invoked from another module

Now looks at OX line of SwissProt record (if present) and checks to see that it refers to a species that we're interested in. If not the xref is not stored.

Added EMBL to list of sources (columns other than name are null, so it is not used as a source to upload from)

Refactored.

SwissProt records with multiple accessions now create appropriate records in the xref and synonym tables