Releases: nmdp-bioinformatics/py-ard
Bug fixes, blend endpoint
blendendpoint added to the service- removed
lgtables and dictionaries. - remove
p_grouptable - store IMGT db version
- Fix XX errors for broad/splits
- Fix loading of IMGT DB version 3130
Shortnulls for exon mode fixed
Ping! Mode and DR Blending
PING mode
- When
ping=Truealleles in P-groups are included in addition to the alleles in G-groups in the corresponding lg/lgx groups.
DR Blending
- Support DRBX Blending from DRB1
`py-ard` REST Service
py-ard REST Service
- REST service with
/redux,/validate,/macendpoints - Run in a Docker container
BugFix for HLA Prefix
Reduce to Shortnulls
Implement shortnulls behavior with new config variable set to True by default.
This will address things like DRB4*01:03N and DRB5*01:08N both in terms of accepting them as valid and also by expanding them as appropriate to the list of longer alleles that have the same expression character.
DRB5*01:08N is acceptable by WHO rules since all suballeles have N.
DRB4*01:03N is acceptable by WMDA (but not WHO) rules but this needs to be handled for things like HF analysis by expansion to something valid (vs rejection) to avoid bias
When there are multiple expression characters in the same group defined by a shortname create multiple shortnulls for the same WHO group. e.g.
{'N', 'L'} A*02:01
{'L', 'Q'} A*02:01:01
{'L', 'Q'} A*24:02
{'L', 'Q'} A*24:02:01
{'L', 'Q'} A*31:01
{'N', 'Q'} A*31:01:02
{'N', 'Q'} B*15:01
{'N', 'Q'} B*15:01:01
{'N', 'Q'} B*44:02
Support shortnull
Implements shortnulls behavior with new config variable set to True by default.
This will address things like DRB4*01:03N and DRB5*01:08N both in terms of accepting them as valid and also by expanding them as appropriate to the list of longer alleles that have the same expression character.
DRB5*01:08N is acceptable by WHO rules since all suballeles have N.
DRB4*01:03N is acceptable by WMDA (but not WHO) rules but this needs to be handled for things like HF analysis by expansion to something valid (vs rejection) to avoid bias
Summary Table for Batch
Show summary table for failed alleles.
Summary
-------
35 alleles failed to reduce.
| Column Name | Allele | Did you mean ?
| --------------- | ---------------- | -------------------------
| r_A_TYPE1 | A*24:09 | A*24:09N
| r_A_TYPE1 | A*33:157 | A*33:157N
| r_A_TYPE1 | A*26:25 | A*26:25N
| r_A_TYPE1 | A*23:19 | A*23:19N
| r_A_TYPE1 | A*24:02:01:02 | A*24:02:01:02L
Fix batch regression error
Fix regression error for MAC reduction #152
Add reduce_2field reduce option
Batch csv pyard-reduce-csv takes in reduce_2field option to reduce 2 fields alleles like B*15:220, DPB1*104:01 and A*02:642