GitLab

ensembl-38'.

Sprout from master 2006-04-18 07:13:35 UTC Glenn Proctor <gp1@sanger.ac.uk> 'Correct documentation for translation() method.'
Delete:
    misc-scripts/protein_match/process_pmach.pl
    modules/Bio/EnsEMBL/DBSQL/Clone.pm
    modules/t/newtransfer.t

Fixed typo in fetch_all_byProbe [ db() -> dbID() ]

added another scalar_attribute rapper get_first_scalar_attibute which gets first non-null value from a list of IDs

Comment out 'print' commands as they bork the web code :(

Added fetch_all_by_logic_name method - "Returns a listref of features created from the database. Only features with an analysis of type $logic_name will be returned."

fetch_by_stable_id_version() now checks if this stable_id.version is actually in the database, and retrieves dbname, release and assembly of latest incarnation of this ID

added optional argument of a compara dbadaptor to get_all_compara_DnaAlignFeatures and get_all_compara_Syntenies to make it easier for users who may not have configured the databases properly

Converted o use pod2usage for the documentation. Added logicname parameter (optional) to allow the analysis type for genes to be specified

added Uniprot/Varsplic to the list of those to get descriptions from. Insert after uniprot but before refseq

unmapped_reasons not generated on the fly now, but have to be uploaded with the update_unmapped_reason.pl script. similar to external_db so that they ids remain the same