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Feature #520

closed

Columns needed in latest-flat.tsv

Added by Madeleine Ball about 13 years ago. Updated about 13 years ago.

Status:
Resolved
Priority:
High
Assigned To:
-
Target version:
-
Story points:
-

Description

We should get the following fields in latest-flat.tsv so we can update gff_getevidence_map.py to use it instead of MySQL. (It's useful to include so the genome report can display allele frequency.):
allele_frequency.num
allele_frequency.denom
qualityscore_penetrance

Consider removing:
qualitycomment_in_silico
qualitycomment_in_vitro
qualitycomment_case_control
qualitycomment_familial
qualitycomment_severity
qualitycomment_treatability

For what it's worth (in case you're thinking about removing other columns), the columns I think gff_getevidence_map.py will use, in addition to the above that are needed, are:
['gene', 'aa_change_short', 'summary_short', 'impact', 'inheritance', 'dbsnp_id', 'qualityscore_in_silico', 'qualityscore_in_vitro', 'qualityscore_case_control', 'qualityscore_familial', 'qualityscore_severity', 'qualityscore_treatability', 'in_omim', 'in_gwas', 'in_pharmgkb', 'genetests_testable', 'genetests_reviewed']

Actions #1

Updated by Madeleine Ball about 13 years ago

  • Priority changed from Normal to High
Actions #2

Updated by Madeleine Ball about 13 years ago

I've pushed my version of gff_getevidence_map.py using a flatfile. It contains changes to download.php that generate a flatfile containing the data it needs. Assuming this works, this can be closed as "wontfix".

Actions #3

Updated by Madeleine Ball about 13 years ago

  • Status changed from New to Resolved
  • Resolution set to wontfix

I ended up making my own flat file, resolving this as wontfix.

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