pyhml 0.0.1

Python HML parser

pyHML

Python HML parser

• Free software: LGPL 3.0

• Documentation: https://pyhml.readthedocs.io.

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
pyhml.tobiotype(hml, outdir, dtype='fasta', by='subject')

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

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

         ID     Locus                             glstring dbversion  \
    0   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
    1   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
    2   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
    3   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0
    4   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
    5   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
    6   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
    7   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0
    8   1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
    9   1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
    10  1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
    11  1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0
    12  1367-7150-8  HLA-DPB1  HLA-DPB1*02:01:02+HLA-DPB1*04:01:01    3.14.0
    13  1367-7150-8  HLA-DPB1  HLA-DPB1*02:01:02+HLA-DPB1*04:01:01    3.14.0
    14  1367-7150-8  HLA-DRB1  HLA-DRB1*03:01:01+HLA-DRB1*07:01:01    3.15.0
    15  1367-7150-8  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 -e 'git+https://github.com/mhalagan-nmdp/pyHML.git#egg=0.0.1'

Credits

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

History

0.0.1 (2017-10-19)

• First release on PyPI.