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.