pipe.  Use the command line switch -compressed with xref_parser.pl to do
this.  The default behaviour (without the -compressed switch) is still
to uncompress gzipped files.

defined, otherwise skip that Xref.

exist.  Otherwise, if a previous file exists (with checkdownload==1),
skipdownload would be 1 and the missing files would not be downloaded...

Fixes spurious FAILs because of missing data.

one-line banner.

Also fixed a old-style test of existance of list elements.

have DR lines).

"perl -MCarp=verbose ...").

Regex fixes ("/\.gz/" --> "/\.gz$/") to be on the safe side.

One instance of forgetting to append directory to file name fixed.

strings.

Small regex tweaks.

New routines to generate the display_xrefs and gene descriptions. This was done incorrectly before or at least inconsistently. Still need to remove comments etc but saving this version for backup

treeshrew and hedgehog added

minor problems (e.g. whitespace after a line-continuation \)

from the sequence-match xref pipeline (they are too for this to be
sensible)

platypus stuff

Changed release to source_release as row name for table source as release became a reserved word in MySQL5

Row name change from release to source_release in source table, this change is done because release became a reserved word in MySQL5

Modifed to code to make it MySQL5 friendly, the changes made were the addition of parenthesis in the LEFT JOIN queries, without the parenthesis the queries will just not work or give unexpected results