pyHML

Python HML parser

• Free software: LGPL 3.0
• Documentation: https://pyhml.readthedocs.io.
• Jupyter Notebook

Features

import pyhml
hml_file = "hml_example.xml"
hmlparser = pyhml.HmlParser()
hml = hmlparser.parse(hml_file)
outdir = 'output/directory'

# Print out each subject in fasta format
hml.tobiotype(outdir, dtype='fasta', by='subject')

# Print out the full HML file in IMGT dat file format
hml.tobiotype(outdir, dtype='imgt', by='file')

# Get pandas DF from HML object
pandasdf = hml.toPandas()
print(pandasdf)

#             ID     Locus                             glstring dbversion  \
# 0   1000-000-0     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
# 1   1000-000-0     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
# 2   1000-000-0     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
# 3   1000-000-0     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
# 4   1000-000-0     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
# 5   1000-000-0     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
# 6   1000-000-0     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
# 7   1000-000-0     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
# 8   1000-000-0     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
# 9   1000-000-0     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
# 10  1000-000-0     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
# 11  1000-000-0     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
# 12  1000-000-0  HLA-DPB1  HLA-DPB1*02:01:02+HLA-DPB1*04:01:01    3.14.0
# 13  1000-000-0  HLA-DPB1  HLA-DPB1*02:01:02+HLA-DPB1*04:01:01    3.14.0
# 14  1000-000-0  HLA-DRB1  HLA-DRB1*03:01:01+HLA-DRB1*07:01:01    3.15.0
# 15  1000-000-0  HLA-DRB1  HLA-DRB1*03:01:01+HLA-DRB1*07:01:01    3.15.0

#                                              sequence
# 0   TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT...
# 1   TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCT...
# 2   TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT...
# 3   GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCA...
# 4   CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG...
# 5   GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG...
# 6   CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG...
# 7   GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG...
# 8   AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC...
# 9   CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA...
# 10  AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC...
# 11  CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA...
# 12  CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...
# 13  CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...
# 14  CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...
# 15  CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...

Install

pip install pyhml

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.