Open rzelayafavila opened 6 years ago
This issue is marked as enhancement
and minor
in bitbucket, but I think its importance should be bumped up, especially as it is causing me problems with the annotation refinery and the cross-reference gene identifiers.
Copied from bitbucket issue #9: (priority: minor) https://bitbucket.org/greenelab/django-genes/issues/9/crossrefdb-names-need-to-match-in-a-case
@mhuyck commented: """ Using
genes_load_geneinfo
on a file for Pseudomonas aeruginosa triggers warnings for each occurrence of a synonym when thegenes_add_xrdb
command was used with the label--name=PseudoCAP
.Although the capitalization "PseudoCAP" is the official label, the Pseudomonas aeruginosa file downloaded from "ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Archaea_Bacteria/Pseudomonas_aeruginosa_PAO1.gene_info.gz " lists the synonyms as "PseudoCap" so matching the CrossRefDB fails. See attached file for a complete list of the errors I received.
Although changing the label to
PseudoCap
should allow the file to load, it may be problematic for matching with other data sources, such as GO. The proposed enhancement here is to makedjango-genes
match this field in a case-insensitive manner wherever relevant. """ Files with the error output are attached in the original bitbucket issue.@mhuyck also commented: "" Capturing this good idea from @cgreene via Slack:
This will probably be a natural consequence of making this field case-insensitive everywhere, but I wanted to not miss this goal.
"""