GitLab

fetach_by_seq_region_id now needed instead of featch_by_region as coords now have id rather than non unique names

'mapper_unique_cache_fix_branch'.

Sprout from master 2006-04-28 13:48:29 UTC Will Spooner <whs@sanger.ac.uk> 'Mapper that runs exonerate jobs using PBS rather than LSF'
Cherrypick from master 2006-05-02 12:40:22 UTC Patrick Meidl <pm2@sanger.ac.uk> 'changes to DBEntryAdaptor->store() and AttributeAdaptor->store()':
    modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
Delete:
    misc-scripts/archive/fake_stable_id_mapping.pl
    misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm
    misc-scripts/assembly/align_by_clone_identity.pl
    misc-scripts/assembly/align_nonident_regions.pl
    misc-scripts/assembly/blastz_matrix.txt
    misc-scripts/assembly/load_alternative_assembly.pl
    misc-scripts/protein_match/process_pmach.pl
    misc-scripts/xref_projection/project_display_xrefs.pl
    misc-scripts/xref_projection/release_37.conf
    misc-scripts/xref_projection/release_38.conf
    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

to fetch ungapped_features from DNA-PEP transcript_supporting_features
(due tothe presence of Insertions that are non modulo-3 in length, which is
common for introns).