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Releases: nmdp-bioinformatics/py-ard

Bug fixes, blend endpoint

09 Feb 14:44
ab2b7b2

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  • blend endpoint added to the service
  • removed lg tables and dictionaries.
  • remove p_group table
  • store IMGT db version
  • Fix XX errors for broad/splits
  • Fix loading of IMGT DB version 3130

Shortnulls for exon mode fixed

18 Nov 23:31
7f6c486

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Ping! Mode and DR Blending

03 Oct 14:30
e1cf309

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PING mode

  • When ping=True alleles 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

10 Jun 19:09
a1074d7

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py-ard REST Service

  • REST service with /redux, /validate, /mac endpoints
  • Run in a Docker container

BugFix for HLA Prefix

19 May 16:02
de3eb47

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Reduce to Shortnulls

29 Mar 18:12
d798dfe

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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

See #154 and #155

Support shortnull

26 Mar 18:16
feaf02b

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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

23 Mar 18:56
dce480b

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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

21 Mar 22:47
429779d

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Fix regression error for MAC reduction #152

Add reduce_2field reduce option

23 Feb 21:12
9620c56

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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