glstring

using the `get_` functions

Each of these functions take a GL String as an argument



In [1]:

    
import glstring
print(glstring.__file__)









    



/Users/bmilius/.virtualenvs/p36/lib/python3.6/site-packages/glstring/__init__.py



In [8]:

    
from glstring.glstring import *
a = "HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03^HLA-B*44:01+HLA-B*44:02"
print(a)









    



HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03^HLA-B*44:01+HLA-B*44:02

`get_alleles()` & `get_loci()`

Each of these functions returns a set of objects.



In [9]:

    
get_alleles(a)









    Out[9]:





{'HLA-A*01:01',
 'HLA-A*01:02',
 'HLA-A*01:03',
 'HLA-A*24:02',
 'HLA-A*24:03',
 'HLA-B*44:01',
 'HLA-B*44:02'}



In [10]:

    
get_loci(a)









    Out[10]:





{'HLA-A', 'HLA-B'}

`get_allele_lists()`, `get_genotypes()`, `get_genotype_lists()`, `get_locus_blocks()`, `get_genotype_blocks()`, & `get_genotype_list_blocks`

Each of these functions return a list of objects found in the GL String.

Locus blocks are separated by a ^.



In [11]:

    
get_locus_blocks(a)









    Out[11]:





['HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03',
 'HLA-B*44:01+HLA-B*44:02']

Genotype list blocks are separated by |



In [13]:

    
get_genotype_list_blocks(a)









    Out[13]:





['HLA-A*01:01/HLA-A*01:02+HLA-A*24:02', 'HLA-A*01:03+HLA-A*24:03']

Genotype blocks are separated by +



In [14]:

    
get_genotype_blocks(a)









    Out[14]:





['HLA-A*01:01/HLA-A*01:02',
 'HLA-A*24:02',
 'HLA-A*01:03',
 'HLA-A*24:03',
 'HLA-B*44:01',
 'HLA-B*44:02']

Genotype lists are found in locus blocks. The contain | delimiters, which separate the possible genotypes. There is one genotype list in this example.



In [15]:

    
get_genotype_lists(a)









    Out[15]:





['HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03']

Genotypes contain a + delimiter and may contain allele lists



In [16]:

    
get_genotypes(a)









    Out[16]:





['HLA-A*01:01/HLA-A*01:02+HLA-A*24:02',
 'HLA-A*01:03+HLA-A*24:03',
 'HLA-B*44:01+HLA-B*44:02']

Allele lists contain a / delimiter



In [17]:

    
get_allele_lists(a)









    Out[17]:





['HLA-A*01:01/HLA-A*01:02']

A more complex example



In [31]:

    
a = ("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~HLA-DRB1*03:01")
print(a)









    



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~HLA-DRB1*03:01



In [32]:

    
get_loci(a)









    Out[32]:





{'HLA-A', 'HLA-B', 'HLA-C', 'HLA-DRB1', 'HLA-DRB5'}



In [33]:

    
get_alleles(a)









    Out[33]:





{'HLA-A*01:01',
 'HLA-A*01:02',
 'HLA-A*01:03',
 'HLA-A*24:02',
 '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-DRB1*03:01',
 'HLA-DRB1*04:07:01',
 'HLA-DRB1*04:92',
 'HLA-DRB5*01:01'}



In [34]:

    
get_allele_lists(a)









    Out[34]:





['HLA-A*01:01/HLA-A*01:02',
 'HLA-B*44:01/HLA-B*44:02',
 'HLA-DRB1*04:07:01/HLA-DRB1*04:92']



In [35]:

    
get_genotypes(a)









    Out[35]:





['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~HLA-DRB1*03:01']



In [36]:

    
get_genotype_lists(a)









    Out[36]:





['HLA-A*01:01/HLA-A*01:02+HLA-A*24:02|HLA-A*01:03+HLA-A*24:03']



In [37]:

    
get_locus_blocks(a)









    Out[37]:





['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~HLA-DRB1*03:01']



In [38]:

    
get_genotypes(get_locus_blocks(a)[0])









    Out[38]:





['HLA-A*01:01/HLA-A*01:02+HLA-A*24:02', 'HLA-A*01:03+HLA-A*24:03']



In [39]:

    
get_genotypes(get_locus_blocks(a)[1])









    Out[39]:





['HLA-B*08:01+HLA-B*44:01/HLA-B*44:02']



In [40]:

    
get_allele_lists(get_genotypes(get_locus_blocks(a)[0])[0])









    Out[40]:





['HLA-A*01:01/HLA-A*01:02']



In [41]:

    
get_alleles(get_allele_lists(get_genotypes(get_locus_blocks(a)[0])[0])[0])









    Out[41]:





{'HLA-A*01:01', 'HLA-A*01:02'}



In [42]:

    
get_haplotypes(a)









    Out[42]:





['HLA-DRB5*01:01~HLA-DRB1*03:01',
 'HLA-DRB1*04:07:01/HLA-DRB1*04:92~HLA-DRB1*03:01']



In [ ]:



In [ ]:

glstring

using the get_ functions

get_alleles() & get_loci()

get_allele_lists(), get_genotypes(), get_genotype_lists(), get_locus_blocks(), get_genotype_blocks(), & get_genotype_list_blocks

A more complex example

using the `get_` functions

`get_alleles()` & `get_loci()`

`get_allele_lists()`, `get_genotypes()`, `get_genotype_lists()`, `get_locus_blocks()`, `get_genotype_blocks()`, & `get_genotype_list_blocks`