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Fix exon reductions for 2 field alleles #322

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Merged
merged 2 commits into from
May 7, 2024
Merged

Fix exon reductions for 2 field alleles #322

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551d8a5
Perform W reductions and then exon reductions when not already in exo…
pbashyal-nmdp May 7, 2024
8646267
Bump version: 1.1.2 → 1.1.3
pbashyal-nmdp May 7, 2024
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ LABEL MAINTAINER="Pradeep Bashyal"

WORKDIR /app

ARG PY_ARD_VERSION=1.1.2
ARG PY_ARD_VERSION=1.1.3

COPY requirements.txt /app
RUN pip install --no-cache-dir --upgrade pip && \
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2 changes: 1 addition & 1 deletion api-spec.yaml
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Expand Up @@ -2,7 +2,7 @@ openapi: 3.0.3
info:
title: ARD Reduction
description: Reduce to ARD Level
version: "1.1.2"
version: "1.1.3"
servers:
- url: 'http://localhost:8080'
tags:
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2 changes: 1 addition & 1 deletion pyard/__init__.py
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Expand Up @@ -26,7 +26,7 @@
from .misc import get_imgt_db_versions as db_versions

__author__ = """NMDP Bioinformatics"""
__version__ = "1.1.2"
__version__ = "1.1.3"


def init(
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11 changes: 9 additions & 2 deletions pyard/ard.py
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Expand Up @@ -258,8 +258,15 @@ def _redux_allele(

return exon_group_allele
else:
# for 'exon' return allele with only first 3 fields
return ":".join(allele.split(":")[0:3])
# Expand to W level and then reduce to exon
w_redux = self.redux(allele, "W")
# If the W redux produces 2 field allele or the same allele,
# don't recurse
if w_redux == allele or len(w_redux.split(":")) == 2:
return allele
else:
# recurse with the W fields
return self.redux(w_redux, "exon")
elif redux_type == "U2":
allele_fields = allele.split(":")
# If resolved out to second field leave alone
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2 changes: 1 addition & 1 deletion setup.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 1.1.2
current_version = 1.1.3
commit = True
tag = True

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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -36,7 +36,7 @@

setup(
name="py-ard",
version="1.1.2",
version="1.1.3",
description="ARD reduction for HLA with Python",
long_description=readme,
long_description_content_type="text/markdown",
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9 changes: 6 additions & 3 deletions tests/features/who.feature
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Expand Up @@ -22,10 +22,13 @@ Feature: WHO expansion and Exon reduction

Scenario Outline: Exon reduction

Exon reductions will expand 2 field alleles to W level before generating
exon level reductions.

Given the typing is <Allele>
When expanding at the <Level> level
Then the expanded allele is found to be <Expanded Alleles>
Examples:
| Allele | Level | Expanded Alleles |
| DRB1*11:01 | exon | DRB1*11:01 |
| A*01:01:01:03 | exon | A*01:01:01 |
| Allele | Level | Expanded Alleles |
| A*01:01:01:03 | exon | A*01:01:01 |
| DRB1*11:01 | exon | DRB1*11:01:01/DRB1*11:01:02/DRB1*11:01:03/DRB1*11:01:04/DRB1*11:01:05/DRB1*11:01:06/DRB1*11:01:07/DRB1*11:01:08/DRB1*11:01:09/DRB1*11:01:10/DRB1*11:01:11/DRB1*11:01:12/DRB1*11:01:13/DRB1*11:01:14/DRB1*11:01:15/DRB1*11:01:16/DRB1*11:01:17/DRB1*11:01:18/DRB1*11:01:19/DRB1*11:01:20/DRB1*11:01:21/DRB1*11:01:22/DRB1*11:01:23/DRB1*11:01:24/DRB1*11:01:25/DRB1*11:01:26/DRB1*11:01:27/DRB1*11:01:28/DRB1*11:01:29/DRB1*11:01:30/DRB1*11:01:31/DRB1*11:01:32/DRB1*11:01:33/DRB1*11:01:34/DRB1*11:01:35/DRB1*11:01:36/DRB1*11:01:37/DRB1*11:01:38/DRB1*11:01:39/DRB1*11:01:40/DRB1*11:01:41/DRB1*11:01:42/DRB1*11:01:43 |