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pyglstring

  • Contains a python package with a module for handling GL Strings, and another for carrying out sanity checks on the string.
  • glstring.glstring
  • glstring.check
  • Three scripts are included.
  • checkgl.py - imports the glstring package. You'll need to install the package by running pip install . from the top of distribution (where the setup.py file is located)
  • checkgl_standalone.py - all necessary function are included
  • checkgl_standalone_DR.py - same as above, but added special warning if genotype has differnt loci, but both are DR.
  • Each of the scripts does a sanity check of a GL String. These check...
  • if any locus is found in more than one locus block
    • good: HLA-A*01:01+HLA-A*24:02^HLA-B*44:01+HLA-B*44:02
    • bad: HLA-A*01:01+HLA-A*24:02^HLA-A*01:03+HLA-A*24:03
  • if any of the following contains more than one locus
  • genotype list
  • good: HLA-A*01:01+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03
  • bad: HLA-A*01:01+HLA-A*24:02|HLA-B*44:01+HLA-B*44:02
  • genotype
  • good: HLA-A*01:01+HLA-A*01:02
  • bad: HLA-A*01:01+HLA-B*01:02
  • allele list
  • good: HLA-B*44:01/HLA-B*44:02
  • but: HLA-B*44:01/HLA-C*44:02

usage

$ ./checkgl.py --help
usage: checkgl.py [-h] -g GLSTRING

optional arguments:
  -h, --help            show this help message and exit
  -g GLSTRING, --glstring GLSTRING
                        GL String to be checked

example with a sane GL String

$ ./checkgl.py -g 'HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03^HLA-B*08:01+HLA-B*44:01/HLA-B*44:02^HLA-C*01:02+HLA-C*01:03^HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92'

GL String = HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03^HLA-B*08:01+HLA-B*44:01/HLA-B*44:02^HLA-C*01:02+HLA-C*01:03^HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92

Checking locus blocks...
HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03
HLA-B*08:01+HLA-B*44:01/HLA-B*44:02
HLA-C*01:02+HLA-C*01:03
HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92
OK: no loci found in more than one locus block

Checking genotype lists ...
('HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03', {'HLA-A'}, 'OK')

Checking genotypes ...
('HLA-A*01:01/HLA-A*01:02+HLA-A*24:02', {'HLA-A'}, 'OK')
('HLA-A*01:03+HLA-A*24:03', {'HLA-A'}, 'OK')
('HLA-B*08:01+HLA-B*44:01/HLA-B*44:02', {'HLA-B'}, 'OK')
('HLA-C*01:02+HLA-C*01:03', {'HLA-C'}, 'OK')
('HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92', {'HLA-DRB5', 'HLA-DRB1'}, 'Phased - Check separately')

Checking allele lists ...
('HLA-A*01:01/HLA-A*01:02', {'HLA-A'}, 'OK')
('HLA-B*44:01/HLA-B*44:02', {'HLA-B'}, 'OK')
('HLA-DRB1*04:07:01/HLA-DRB1*04:92', {'HLA-DRB1'}, 'OK')

example with a problem GL String

$ ./checkgl.py -g 'HLA-A*01:01/HLA-B*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03^HLA-B*08:01+HLA-B*44:01/HLA-B*44:02^HLA-C*01:02+HLA-A*01:01~HLA-C*01:03^HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92'

GL String = HLA-A*01:01/HLA-B*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03^HLA-B*08:01+HLA-B*44:01/HLA-B*44:02^HLA-C*01:02+HLA-A*01:01~HLA-C*01:03^HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92

Checking locus blocks...
HLA-A*01:01/HLA-B*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03
HLA-B*08:01+HLA-B*44:01/HLA-B*44:02
HLA-C*01:02+HLA-A*01:01~HLA-C*01:03
HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92
WARNING: Loci found in more than 1 locus block: {'HLA-B', 'HLA-A'}

Checking genotype lists ...
('HLA-A*01:01/HLA-B*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03', {'HLA-B', 'HLA-A'}, 'WARNING')

Checking genotypes ...
('HLA-A*01:01/HLA-B*01:02+HLA-A*24:02', {'HLA-B', 'HLA-A'}, 'Unphased - WARNING')
('HLA-A*01:03+HLA-A*24:03', {'HLA-A'}, 'OK')
('HLA-B*08:01+HLA-B*44:01/HLA-B*44:02', {'HLA-B'}, 'OK')
('HLA-C*01:02+HLA-A*01:01~HLA-C*01:03', {'HLA-C', 'HLA-A'}, 'Phased - Check separately')
('HLA-DRB5*01:01~HLA-DRB1*03:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92', {'HLA-DRB5', 'HLA-DRB1'}, 'Phased - Check separately')

Checking allele lists ...
('HLA-A*01:01/HLA-B*01:02', {'HLA-B', 'HLA-A'}, 'WARNING')
('HLA-B*44:01/HLA-B*44:02', {'HLA-B'}, 'OK')
('HLA-DRB1*04:07:01/HLA-DRB1*04:92', {'HLA-DRB1'}, 'OK')