Python HML parser
Project description
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 pyhml
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.
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