[GENE_DESCRIPTIONS] GFF = [ 1 DAUGHTER->product /(.+)/ ] [TRANSCRIPT_DESCRIPTIONS] GFF = [ 1 SELF->product /(.+)/ ]
Descriptions are displayed in the Ensembl website and included in the search index (optional Step 2.8). Each set of descriptions may be sourced from any number of files, in which case the first number in the value array indicates the priority accorded to descriptions from that source. Descriptions from sources with lower numbers will overwrite those from sources with higher numbers. If set to 1 this priority flag will also cause any existing descriptions in the database for the current gene/transcript to be overwritten.
_DESCRIPTIONS from files other than
.gff must be linked to the correct feature by [_STABLE_IDS] (where linking files by
_STABLE_IDS is described in more detail):
[FILES] GFF = [ gff http://example.com/gene_models.gff3.gz ] PROTEIN = [ fa http://example.com/proteins.fa.gz ] ANNOTATION = [ tsv http://example.com/annotations.txt.gz ] [GENE_STABLE_IDS] GFF = [ gene->Name /(.+)/ ] PROTEIN = [ DISPLAY_ID /(.+)-PA/ ] ANNOTATION = [ FIELD_1 /(.+)/ ] [GENE_DESCRIPTIONS] GFF = [ 1 DAUGHTER->product /(.+)/ ] PROTEIN = [ 2 DESCRIPTION /(.+)/ ] ANNOTATION = [ 3 FIELD_2 /(.+)/ ]
ANNOTATIONfile has the lowest priority (
3) and descriptions from
FIELD_2in this file will only be used if no corresponding description is found in either of the other files
PROTEINfile has priority
2so descriptions from the second part of the
fastaheaders will be used in preference to descriptions in the
ANNOTATIONfile unless a description exists in the
GFFfile has priority
1so descriptions from this file will be used in preference to those from the other files and if a description already exists for this gene in the database, it will be overwritten by this new value.
- reducing all the priorities by 1 would retain the same behaviour with the exception that existing descriptions in the database would not be overwritten.
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