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IMGT URL fix for 0.6.x release #138

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Merged
merged 3 commits into from
Jan 24, 2022
Merged

IMGT URL fix for 0.6.x release #138

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56fb5af
Only import openpyxl for Excel
pbashyal-nmdp Dec 13, 2021
e7bdeaf
Change IMGT URL for /allelelist directory
pbashyal-nmdp Jan 24, 2022
0855feb
Bump version: 0.6.10 → 0.6.11
pbashyal-nmdp Jan 24, 2022
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2 changes: 1 addition & 1 deletion pyard/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,4 +24,4 @@
from .pyard import ARD

__author__ = """NMDP Bioinformatics"""
__version__ = '0.6.10'
__version__ = '0.6.11'
4 changes: 2 additions & 2 deletions pyard/data_repository.py
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Expand Up @@ -192,7 +192,7 @@ def generate_alleles_and_xx_codes_and_who(db_connection: sqlite3.Connection, img
# date: 2017-07-10
# version: IPD-IMGT/HLA 3.29.0
# origin: https://github.com/ANHIG/IMGTHLA/Allelelist.3290.txt
# repository: https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/Allelelist.3290.txt
# repository: https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/allelelist/Allelelist.3290.txt
# author: WHO, Steven G. E. Marsh (steven.marsh@ucl.ac.uk)
AlleleID,Allele
HLA00001,A*01:01:01:01
Expand Down Expand Up @@ -228,7 +228,7 @@ def generate_alleles_and_xx_codes_and_who(db_connection: sqlite3.Connection, img
if imgt_version == "Latest":
allele_list_url = f'{IMGT_HLA_URL}Latest/Allelelist.txt'
else:
allele_list_url = f'{IMGT_HLA_URL}Latest/Allelelist.{imgt_version}.txt'
allele_list_url = f'{IMGT_HLA_URL}Latest/allelelist/Allelelist.{imgt_version}.txt'
allele_df = pd.read_csv(allele_list_url, header=6, usecols=['Allele'])

# Create a set of valid alleles
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15 changes: 8 additions & 7 deletions scripts/pyard-reduce-csv
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Expand Up @@ -176,13 +176,14 @@ if __name__ == '__main__':
verbose = ard_config["verbose_log"]
white_space_regex = re.compile(r"\s+")

try:
import openpyxl
except ImportError:
print("For Excel output, openpyxl library needs to be installed. "
"Install with:")
print(" pip install openpyxl")
sys.exit(1)
if ard_config["output_file_format"] == 'xlsx':
try:
import openpyxl
except ImportError:
print("For Excel output, openpyxl library needs to be installed. "
"Install with:")
print(" pip install openpyxl")
sys.exit(1)

# Instantiate py-ard object with the latest
ard = pyard.ARD()
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2 changes: 1 addition & 1 deletion setup.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.6.10
current_version = 0.6.11
commit = True
tag = True

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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -42,7 +42,7 @@

setup(
name='py-ard',
version='0.6.10',
version='0.6.11',
description="ARD reduction for HLA with Python",
long_description=readme + '\n\n' + history,
author="CIBMTR",
Expand Down