GitLab

ensemblgenomes-9-62'.

Sprout from master 2011-04-19 12:20:57 UTC Monika Komorowska <mk8@sanger.ac.uk> 'Added procedure file parameter.'
Delete:
    misc-scripts/protein_match/process_pmach.pl

Test case addition to make sure we don't keep on iterating executing the transaction when its been successful

Added code to fix issue with Corf genes in zebrafish. The gene names were not being modified to look like hsC*orf*-like. This now works.

Added an additional check in the transform method. When testing exons, if consecutive exons in the old version of the transcript were on the same strand then the new versions should be on the same strand too. If not, returns undef. Prevents cases being transformed where the transcript's exons map as below:

1
------------------------------
-1        5  4  3  2  1

to

1      3  4  5
------------------------------
-1               2  1

Replace HGNC_ENSTParser.pm, GI_Vega_Parser.pm and ZFIN_DARTParser.pm parsers with VegaOfficialNameParser.pm

CV: ----------------------------------------------------------------------

changed the dumped databases entrys from int to enum so changed the values here to match those in the database

Add abillity to ignore a black list of genes for dumping. Also new methos to get a hash of the non reference alt_alleles

changed the dumped databases entrys form int to enum so changed the values here to match those in the database

New table alt_allele added and dumped in the xref table changed to an enum for ease of use/understabding