#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Oct 8 13:24:16 2017
@author: hhuang2
"""
from utils import IMGTdbIO
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
typing1 = 'A*23:17'
Refseq1 = IMGTdbIO.readIMGTsql(typing1, db_fp= '../Database/', field = 'Exon1, Exon2, Exon3, Exon4, Exon5, Exon6, Exon7, Exon8')
typing2 = 'A*23:01:01'
Refseq2 = IMGTdbIO.readIMGTsql(typing2, db_fp= '../Database/', field = 'Exon1, Exon2, Exon3, Exon4, Exon5, Exon6, Exon7, Exon8')
coding_dna = Seq(Refseq1, generic_dna)
coding_dna.translate()
str(coding_dna.translate())
seq = ''
for i in range(len(Refseq1)):
seq += Refseq1[i]
typing1 = 'A*23:17'
typing2 = 'A*23:01:01'
HLAtyping = typing1+'_'+typing2
Exons = 'Exon1, Exon2, Exon3, Exon4, Exon5, Exon6, Exon7, Exon8'
def check_twoBlock_seq(seq_count,
tplist,
unique_Query,
unique_HLATyping_list,
ID,
version="3310"):
'''
Two blocks one phase sequences
'''
if type(ID) == float:
ID = str(int(ID))
Locus = tplist[0].split("*")[0]
ARS0seq = IMGTdbIO.readIMGTsql(tplist[0],
field='Exon2, Exon3',
version=version)
ARS1seq = IMGTdbIO.readIMGTsql(tplist[1],
field='Exon2, Exon3',
version=version)
if seq_count > 4:
print("Please check the ID: " + ID + " Locus " + Locus +
"! More sequences than expected.")
QueryTyping = {}
for seq_item in unique_Query:
if ARS0seq[0] in seq_item: # the first type; block 1; exon2
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
else: # altered block order
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item, QueryTyping["PS1"]["Sequence"][0]],
"blockIDs": [1, 2]
}
elif ARS0seq[1] in seq_item: # the first type; block 2; exon3
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [2]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
elif ARS1seq[0] in seq_item: # second type; block 1; exon2
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item, QueryTyping["PS2"]["Sequence"][0]],
"blockIDs": [1, 2]
}
elif ARS1seq[1] in seq_item: # second type; block2; exon3
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [2]
}
else:
QueryTyping["PS2"]['Sequence'].append(seq_item)
QueryTyping["PS2"]['blockIDs'].append(2)
else:
QueryTyping["PS3"] = {
"GLstring": unique_HLATyping_list,
"Sequence": [seq_item],
"blockIDs": [1]
}
print(ID + ": The sequence at Locus " + Locus +
" doesn't match to either of the Typings")
if "PS1" in QueryTyping.keys() and "PS2" not in QueryTyping.keys(
): ## Homozygous
QueryTyping["PS2"] = QueryTyping["PS1"]
return (QueryTyping)
def check_DQB102_Block_seq(seq_count,
tplist,
unique_Query,
unique_HLATyping_list,
ID,
version="3310"):
'''
Two blocks one phase sequences
'''
if type(ID) == float:
ID = str(int(ID))
Locus = tplist[0].split("*")[0]
ARS0seq = IMGTdbIO.readIMGTsql(tplist[0],
field='Exon2, Exon3',
version=version)
ARS1seq = IMGTdbIO.readIMGTsql(tplist[1],
field='Exon2, Exon3',
version=version)
serotype = [tp.split(":")[0] for tp in tplist]
if seq_count > 3:
print(
"Please check the ID: " + ID + " Locus " + Locus +
", have heterozygotic DQB1*02 types or have more sequences than expected."
)
QueryTyping = {}
for seq_item in unique_Query:
# PS1
if ARS0seq[0] in seq_item: # PS1 Exon 2
if serotype[0] == "DQB1*02": # DQB1*02 - 2 blocks
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
else: # altered block order
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence":
[seq_item, QueryTyping["PS1"]["Sequence"][0]],
"blockIDs": [1, 2]
}
else: # non-DQB1 - 1 block
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
elif ARS0seq[1] in seq_item: # PS1 Exon 3
if serotype[0] == "DQB1*02": # DQB1*02 - 2 blocks
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [2]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
else: # non-DQB1 - 1 block
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
## PS2
elif ARS1seq[0] in seq_item: # PS2 Exon 2
if serotype[0] == "DQB1*02": # DQB1*02 - 2 blocks
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else: # altered block order
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence":
[seq_item, QueryTyping["PS2"]["Sequence"][0]],
"blockIDs": [1, 2]
}
else: # non-DQB1 - 1 block
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS2"]['Sequence'].append(seq_item)
QueryTyping["PS2"]['blockIDs'].append(2)
elif ARS1seq[1] in seq_item: # PS2 Exon 3
if serotype[0] == "DQB1*02": # DQB1*02 - 2 blocks
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [2]
}
else:
QueryTyping["PS2"]['Sequence'].append(seq_item)
QueryTyping["PS2"]['blockIDs'].append(2)
else: # non-DQB1 - 1 block
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS2"]['Sequence'].append(seq_item)
QueryTyping["PS2"]['blockIDs'].append(2)
else:
QueryTyping["PS3"] = {
"GLstring": unique_HLATyping_list,
"Sequence": [seq_item],
"blockIDs": [1]
}
print(ID + ": The sequence at Locus " + Locus +
" doesn't match to either of the Typings")
if "PS1" in QueryTyping.keys() and "PS2" not in QueryTyping.keys(
): ## Homozygous
QueryTyping["PS2"] = QueryTyping["PS1"]
return (QueryTyping)
def check_oneBlock_seq(seq_count,
tplist,
unique_Query,
unique_HLATyping_list,
ID,
version="3310"):
'''
For one block one phase sequence
'''
if type(ID) == float:
ID = str(int(ID))
Locus = tplist[0].split("*")[0]
ARS0seq = IMGTdbIO.readIMGTsql(tplist[0],
field='Exon2, Exon3',
version=version)
ARS1seq = IMGTdbIO.readIMGTsql(tplist[1],
field='Exon2, Exon3',
version=version)
if seq_count > 2:
print("Please check the ID: " + ID + " Locus " + Locus +
"! More sequences than expected.")
QueryTyping = {}
for seq_item in unique_Query:
if ARS0seq != ARS1seq: # if the two types have different ARS regions
if ARS0seq[0] in seq_item and ARS0seq[
1] in seq_item: # the first type
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
elif ARS1seq[0] in seq_item and ARS1seq[
1] in seq_item: # second type
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS2"]['Sequence'].append(seq_item)
QueryTyping["PS2"]['blockIDs'].append(2)
else:
if "PS3" not in QueryTyping.keys():
QueryTyping["PS3"] = {
"GLstring": unique_HLATyping_list,
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS3"]['Sequence'].append(seq_item)
QueryTyping["PS3"]['blockIDs'].append(2)
print(ID + ": The sequence at Locus " + Locus +
" doesn't match to either of the Typings")
else: # if the two types have the same ARS regions
ARS0seq1456 = IMGTdbIO.readIMGTsql(
tplist[0], field='Exon1, Exon4, Exon5, Exon6', version=version)
ARS1seq1456 = IMGTdbIO.readIMGTsql(
tplist[1], field='Exon1, Exon4, Exon5, Exon6', version=version)
if ARS0seq1456 != ARS1seq1456:
if ARS0seq1456[0] in seq_item and ARS0seq1456[
1] in seq_item and ARS0seq1456[
2] in seq_item and ARS0seq1456[
3] in seq_item: # the first type
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
elif ARS1seq1456[0] in seq_item and ARS1seq1456[
1] in seq_item and ARS1seq1456[
2] in seq_item and ARS1seq1456[
3] in seq_item: # second type
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS2"]['Sequence'].append(seq_item)
QueryTyping["PS2"]['blockIDs'].append(2)
else:
if "PS3" not in QueryTyping.keys():
QueryTyping["PS3"] = {
"GLstring": unique_HLATyping_list,
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS3"]['Sequence'].append(seq_item)
QueryTyping["PS3"]['blockIDs'].append(2)
print(ID + ": The sequence at Locus " + Locus +
" doesn't match to either of the Typings")
else:
ARS0seq7 = IMGTdbIO.readIMGTsql(tplist[0],
field='Exon7',
version=version)
ARS1seq7 = IMGTdbIO.readIMGTsql(tplist[1],
field='Exon7',
version=version)
if ARS0seq7 != ARS1seq7:
if ARS0seq7[0] in seq_item: # the first type
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
elif ARS1seq7[0] in seq_item: # second type
if "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS2"]['Sequence'].append(seq_item)
QueryTyping["PS2"]['blockIDs'].append(2)
else:
QueryTyping["PS3"] = {
"GLstring": unique_HLATyping_list,
"Sequence": [seq_item],
"blockIDs": [1]
}
print(ID + ": The sequence at Locus " + Locus +
" doesn't match to either of the Typings")
else: ## all 8 exons are the same
if "PS1" not in QueryTyping.keys():
QueryTyping["PS1"] = {
"GLstring": unique_HLATyping_list[0],
"Sequence": [seq_item],
"blockIDs": [1]
}
elif "PS2" not in QueryTyping.keys():
QueryTyping["PS2"] = {
"GLstring": unique_HLATyping_list[1],
"Sequence": [seq_item],
"blockIDs": [1]
}
else:
QueryTyping["PS1"]['Sequence'].append(seq_item)
QueryTyping["PS1"]['blockIDs'].append(2)
print(
ID + ": The sequence at Locus " + Locus +
" two typings have exactly the same Exon sequences. Cannot distinguish by Exons."
)
if "PS1" in QueryTyping.keys() and "PS2" not in QueryTyping.keys(
): ## Homozygous
QueryTyping["PS2"] = QueryTyping["PS1"]
return (QueryTyping)