GitLab

--cleanup is specified on the command line.

Fetch uniprot.txt rather than swissprot.txt which does not exist on the
zfin.org HTTP server anymore.  Modify the ZFINParser accordingly (it
contains hardcoded file names) and use catfile() rather than manual
concatentation of file paths.

Add special source 'IMGT/LIGM_DB' (assumed to exist by SegmentParser,
but not explicitly connected with any species).

Collapse lists of data URIs by means of FTP file name globbing,
especially for the various RefSeq sources.

Updated some URIs to point to new data (e.g. FlyBase for Drosophila).

Make fetch_files() understand file name globbing for FTP transfers (will
not work for HTTP).

Make the command line switches --delete_downloaded and --cleanup work as
expected.

No longer mandatory to specify compara database on command-line; will use first one defined in registry file if not specified on the command line.

let a species have multiple 'taxonomy_id' entries, one for each strain.

Change anopheles configuration to comply to this.

Change Perl script to take care of this as well.

'xref_config.ini' using the 'xref_confg2sql.pl' script.

New key: 'strain_of' (used for anopheles strain).

*** HEADS UP ***

The xref_parser will now croak if used with the old
populate_metadata.sql file.

Make name2species_id() also consider aliases (this is currently comment
out).

Stub for fetch_file() method that will eventually handle downloading of
data.

Minor cleanup.

unbreaks RefSeq vertibrate_mammalian, vertibrate_other, invertibrate,
and fungi Xref runs.

Add RefSeq data files that do exists but that we don't list.

around the messed up the anopheles Xref run where sources would be used
twice.

Also make the needed changes to the conversion script.

Also renamed these sources as they now are MULTI sources (this is just a
label, but it's better than calling them 'homo_sapiens').

Added CCDS and OTTT entries for mouse

parsing.

protein_id_predicted.

Shuffle.