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NomenCleaner.py
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# -*- coding: utf-8 -*-
import os, sys, re
import argparse, textwrap
import pandas as pd
########## < Core Global Variables > ##########
std_MAIN_PROCESS_NAME = "[%s]: " % (os.path.basename(__file__))
std_ERROR_MAIN_PROCESS_NAME = "\n[%s::ERROR]: " % (os.path.basename(__file__))
std_WARNING_MAIN_PROCESS_NAME = "\n[%s::WARNING]: " % (os.path.basename(__file__))
HLA_names = ["A", "B", "C", "DPA1", "DPB1", "DQA1", "DQB1", "DRB1"]
header_ped = ["FID", "IID", "PID", "MID", "Sex", "Phe"]
# Patterns
p_Suffix = re.compile(r'.+[A-Z]$')
p_Prefix = re.compile(r'^\w+\*')
class HATK_NomenCleaner(object):
def __init__(self, _hped, _hat, _out, **kwargs):
"""
"""
if not os.path.exists(_hped):
print(std_ERROR_MAIN_PROCESS_NAME + "Given HPED file('{}') doesn't exist.\n"
"Please check the '--hped' argument again.\n"
"".format(_hped))
sys.exit()
else:
# Checking the number of columns
f_hped = open(_hped, 'r')
hped_1st_line = f_hped.readline()
hped_1st_line = re.split(pattern='\s+', string=hped_1st_line.rstrip('\n'))
if len(hped_1st_line) != 22:
# # of columns of hped file must be 22(6 + 8*2).
print(std_ERROR_MAIN_PROCESS_NAME + "The number of columns of given HPED file('{}') must be 22 but it is '{}'.\n"
"Please check the number of columns of that HPED file again."
"".format(_hped, len(hped_1st_line)))
sys.exit()
if not os.path.exists(_hat):
print(std_ERROR_MAIN_PROCESS_NAME + "Given HAT(HLA Allel Table) file('{}') doesn't exist.\n"
"Please check the '--hat")
self.chped = NomenCleaner(_hped, _hat, _out,
__oneF=kwargs['__oneF'], __twoF=kwargs['__twoF'], __threeF=kwargs['__threeF'], __fourF=kwargs['__fourF'],
__Ggroup=kwargs['__Ggroup'], __Pgroup=kwargs['__Pgroup'],
__f_NoCaption=kwargs["__f_NoCaption"], __leave_NotFound=kwargs["__leave_NotFound"])
def NomenCleaner(_hped, _hat, _out, __f_NoCaption=False, __leave_NotFound=False, **kwargs):
##### < Output Format > #####
FIELD = ''
if kwargs['__oneF']:
OUTPUT_FORMAT = 1
FIELD = 'Maximum 1 field'
elif kwargs['__twoF']:
OUTPUT_FORMAT = 2
FIELD = 'Maximum 2 fields'
elif kwargs['__threeF']:
OUTPUT_FORMAT = 3
FIELD = 'Maximum 3 fields'
elif kwargs['__fourF']:
OUTPUT_FORMAT = 4
FIELD = 'Maximum 4 fields'
elif kwargs['__Ggroup']:
OUTPUT_FORMAT = 5
FIELD = 'G code'
elif kwargs['__Pgroup']:
OUTPUT_FORMAT = 6
FIELD = 'P code'
else:
# Default mode
OUTPUT_FORMAT = 0
if OUTPUT_FORMAT != 0:
print(std_MAIN_PROCESS_NAME + "Generating CHPED with {} HLA alleles.".format(FIELD))
##### < Loading Data > #####
# *.hped
__HPED__ = pd.read_csv(_hped, sep='\s+', header=None, dtype=str)
# print("__HPED__ :\n{}\n".format(__HPED__.head()))
# *.hat
__HAT__ = pd.read_csv(_hat, sep='\s+', header=0, dtype=str, index_col=0)
# print("__HAT__ :\n{}\n".format(__HAT__.head()))
d__HAT__ = {HLA_names[i]: __HAT__.loc[HLA_names[i], :] for i in range(len(HLA_names))}
# for k,v in d__HAT__.items():
# print("HLA : {}\n{}\n".format(k, v.head()))
##### < Main iteration > #####
f_chped = open(_out+'.chped', 'w')
f_chped_log = open(_out+'.chped.log', 'w')
count = 0
for eachRow in __HPED__.itertuples():
# print(eachRow)
[t_FID, t_IID] = eachRow[1:3]
t_alleles = eachRow[7:]
t_alleles = list(map(lambda x : p_Prefix.sub(string=x, repl=''), t_alleles)) # Ripping off gene prefix
# print(t_alleles)
### [1] Allele conversion
l_alleles_row = []
for i in range(len(HLA_names)):
idx1 = 2*i
idx2 = 2*i + 1
# chromosome 1
if t_alleles[idx1] != '0':
[t_converted_allele1, LOG_MESSAGE1] = getConvertedAllele2(HLA_names[i], t_alleles[idx1], d__HAT__[HLA_names[i]], OUTPUT_FORMAT, __leave_NotFound)
# print("Converted Alleles : {}".format(t_converted_allele1))
# print("LOG_MESSAGE :{}\n".format(LOG_MESSAGE1))
else:
t_converted_allele1 = t_alleles[idx1]
LOG_MESSAGE1 = 'No conversion ({})'.format(t_alleles[idx1])
# chromosome 2
if t_alleles[idx2] != '0':
[t_converted_allele2, LOG_MESSAGE2] = getConvertedAllele2(HLA_names[i], t_alleles[idx2], d__HAT__[HLA_names[i]], OUTPUT_FORMAT, __leave_NotFound)
# print("Converted Alleles : {}".format(t_converted_allele2))
# print("LOG_MESSAGE :{}\n".format(LOG_MESSAGE2))
else:
t_converted_allele2 = t_alleles[idx2]
LOG_MESSAGE2 = 'No conversion ({})'.format(t_alleles[idx2])
l_alleles_row.append(('%s*'%(HLA_names[i]) if (not __f_NoCaption and t_converted_allele1 != '0') else '') + t_converted_allele1)
l_alleles_row.append(('%s*'%(HLA_names[i]) if (not __f_NoCaption and t_converted_allele2 != '0') else '') + t_converted_allele2)
### [2] logging the result
f_chped_log.write('\t'.join([t_FID, t_IID, HLA_names[i]+'_1', LOG_MESSAGE1])+'\n')
f_chped_log.write('\t'.join([t_FID, t_IID, HLA_names[i]+'_2', LOG_MESSAGE2])+'\n')
### Generating chped
f_chped.write('\t'.join(list(eachRow[1:7]) + l_alleles_row) + '\n')
count += 1
# if count > 1 : break
f_chped.close()
f_chped_log.close()
return _out+'.chped'
def getConvertedAllele2(_hla, _allele, _d__HAT__, _OUTPUT_FORMAT, __leave_NotFound):
__RETURN__ = None # Converted allele
LOG_MESSAGE = None
### < Setting `_from` > ###
# `_from` := 'STANDARD', 'OLD', 'Ggroup' or 'Pgroup' column in HAT file.
if _allele.endswith('G'):
_from = 'Ggroup'
elif _allele.endswith('P'):
_from = 'Pgroup'
else:
if ':' in _allele:
_from = 'STANDARD'
else:
_from = 'OLD'
if ':' in _allele:
# Colon (either STANDARD, G-group or P-group).
[__RETURN__, LOG_MESSAGE] = get1stAllele2(_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
# No colon (either OLD or STANDARD).
# Assumes it OLD first.
if len(_allele) <= 3:
# Exception handling for 1field allele (ex. DPB1*03 -> 0302(-> 102:01; OLD) / 03:01:01:01(STANDARD))
# G-group and P-group alleles can't be here naturally. (ex. 0101P(01:01P) ... at least 5 characters.)
flag_matched_STANDARD = _d__HAT__['STANDARD'].str.match(_allele)
# Check both first.
if flag_matched_STANDARD.any():
# Give priority to 'STANDARD' over 'OLD'.
[__RETURN__, LOG_MESSAGE] = get1stAllele2(_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
[__RETURN__, LOG_MESSAGE] = get1stAllele2(_allele, _d__HAT__, 'OLD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
### Possibly OLD nomenclature
# flag_matched_OLD = _d__HAT__[_from].str.match(_allele)
flag_matched_OLD = _d__HAT__['OLD'].str.match(_allele).any()
flag_matched_STANDARD = False
## Checking Suffix
hasSuffix = p_Suffix.match(_allele)
if hasSuffix:
_allele2 = _allele[:-1]
_allele_Suffix = _allele[-1]
else:
_allele2 = _allele
_allele_Suffix = -1
### Main Digit-checking
sr_TEMP = _d__HAT__['STANDARD'].str
if len(_allele2) == 4:
# 2 + 2 (+C) = 4
trial1_allele = ':'.join([_allele2[:2], _allele2[2:4]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 5:
# (1) 2 + 3 (+C) = 5
# (2) 3 + 2 (+C) = 5
trial1_allele = ':'.join([_allele2[:2], _allele2[2:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
trial2_allele = ':'.join([_allele2[:3], _allele2[3:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 6:
# (1) 2 + 2 + 2 (+C)
# (2) 3 + 3 (+C)
# (1) 2 + 2 + 2 (+C)
trial1_allele = ':'.join([_allele2[:2], _allele2[2:4], _allele2[4:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
# (2) 3 + 3 (+C)
trial2_allele = ':'.join([_allele2[:3], _allele2[3:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 7:
# (1) 2 + 3 + 2 (+C) = 7
# (2) 2 + 2 + 3 (+C) = 7
# (3) 3 + 2 + 2 (+C) = 7
# (1) 2 + 3 + 2 (+C) = 7
trial1_allele = ':'.join([_allele2[:2], _allele2[2:5], _allele2[5:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
# (2) 2 + 2 + 3 (+C) = 7
trial2_allele = ':'.join([_allele2[:2], _allele2[2:4], _allele2[4:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
# (3) 3 + 2 + 2 (+C) = 7
trial3_allele = ':'.join([_allele2[:3], _allele2[3:5], _allele2[5:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial3 = sr_TEMP.match(trial3_allele)
if Flag_trial3.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial3_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 8:
# (1) 2 + 2 + 2 + 2 (+C)
# (2) 3 + 2 + 3 (+C)
# (3) 3 + 3 + 2 (+C)
# (1) 2 + 2 + 2 + 2
trial1_allele = ':'.join([_allele2[:2], _allele2[2:4], _allele2[4:6], _allele2[6:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
# (2) 3 + 2 + 3
trial2_allele = ':'.join([_allele2[:3], _allele2[3:5], _allele2[5:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
# (3) 3 + 3 + 2
trial3_allele = ':'.join([_allele2[:3], _allele2[3:6], _allele2[6:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial3 = sr_TEMP.match(trial3_allele)
if Flag_trial3.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial3_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 9:
# (1) 2 + 3 + 2 + 2 (+C)
# (2) 3 + 2 + 2 + 2 (+C)
# (1) 2 + 3 + 2 + 2
trial1_allele = ':'.join([_allele2[:2], _allele2[2:5], _allele2[5:7], _allele2[7:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
# (2) 3 + 2 + 2 + 2
trial2_allele = ':'.join([_allele2[:3], _allele2[3:5], _allele2[5:7], _allele2[7:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 10:
# (1) 3 + 3 + 2 + 2
trial1_allele = ':'.join([_allele2[0:3], _allele2[3:6], _allele2[6:8], _allele2[8:10]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, 'STANDARD', _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
flag_matched_STANDARD = True
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
if flag_matched_OLD and flag_matched_STANDARD:
"""
(2020. 05. 15.)
ex. HLA-B: 0702
OLD -> STANDARD : 070202 -> 07:02:02 ... (1)
STANDARD : 07:02:01:01 ... (2) => This is proper.
"""
# Need to check respective STANDARD names first.
[return_old, log_message_old] = get1stAllele2(_allele, _d__HAT__, 'OLD', 4, __leave_NotFound, _allele0=_allele)
[return_standard, log_message_standard] = [__RETURN__, LOG_MESSAGE]
if return_old <= return_standard:
# (e.g.) 07:02:01:01 < 07:02:02
if _OUTPUT_FORMAT == 4:
return [return_old, log_message_old]
else:
_from = 'OLD'
else:
if _OUTPUT_FORMAT == 4:
return [return_standard, log_message_standard]
else:
_from = 'STANDARD'
elif flag_matched_OLD and not flag_matched_STANDARD:
# Only found in OLD
_from = 'OLD'
elif not flag_matched_OLD and flag_matched_STANDARD:
# Only found in STANDARD
_from = 'STANDARD'
else:
# Wrong. Maybe not in the given IMGT version.
if __leave_NotFound:
return [_allele, '[Leave Not Found] {} -> {}'.format(_allele, _allele)]
else:
return ['0', "[Not Found] {} -> 0".format(_allele)]
if _from == 'OLD':
[__RETURN__, LOG_MESSAGE] = get1stAllele2(_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
## Checking Suffix
hasSuffix = p_Suffix.match(_allele)
if hasSuffix:
_allele2 = _allele[:-1]
_allele_Suffix = _allele[-1]
else:
_allele2 = _allele
_allele_Suffix = -1
### Main Digit-checking
sr_TEMP = _d__HAT__[_from].str
if len(_allele2) == 4:
# 2 + 2 (+C) = 4
trial1_allele = ':'.join([_allele2[:2], _allele2[2:4]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 5:
# (1) 2 + 3 (+C) = 5
# (2) 3 + 2 (+C) = 5
trial1_allele = ':'.join([_allele2[:2], _allele2[2:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
trial2_allele = ':'.join([_allele2[:3], _allele2[3:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 6:
# (1) 2 + 2 + 2 (+C)
# (2) 3 + 3 (+C)
# (1) 2 + 2 + 2 (+C)
trial1_allele = ':'.join([_allele2[:2], _allele2[2:4], _allele2[4:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
# (2) 3 + 3 (+C)
trial2_allele = ':'.join([_allele2[:3], _allele2[3:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 7:
# (1) 2 + 3 + 2 (+C) = 7
# (2) 2 + 2 + 3 (+C) = 7
# (3) 3 + 2 + 2 (+C) = 7
# (1) 2 + 3 + 2 (+C) = 7
trial1_allele = ':'.join([_allele2[:2], _allele2[2:5], _allele2[5:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
# (2) 2 + 2 + 3 (+C) = 7
trial2_allele = ':'.join([_allele2[:2], _allele2[2:4], _allele2[4:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
# (3) 3 + 2 + 2 (+C) = 7
trial3_allele = ':'.join([_allele2[:3], _allele2[3:5], _allele2[5:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial3 = sr_TEMP.match(trial3_allele)
if Flag_trial3.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial3_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 8:
# (1) 2 + 2 + 2 + 2 (+C)
# (2) 3 + 2 + 3 (+C)
# (3) 3 + 3 + 2 (+C)
# (1) 2 + 2 + 2 + 2
trial1_allele = ':'.join([_allele2[:2], _allele2[2:4], _allele2[4:6], _allele2[6:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
# (2) 3 + 2 + 3
trial2_allele = ':'.join([_allele2[:3], _allele2[3:5], _allele2[5:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
# (3) 3 + 3 + 2
trial3_allele = ':'.join([_allele2[:3], _allele2[3:6], _allele2[6:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial3 = sr_TEMP.match(trial3_allele)
if Flag_trial3.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial3_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 9:
# (1) 2 + 3 + 2 + 2 (+C)
# (2) 3 + 2 + 2 + 2 (+C)
# (1) 2 + 3 + 2 + 2
trial1_allele = ':'.join([_allele2[:2], _allele2[2:5], _allele2[5:7], _allele2[7:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
# (2) 3 + 2 + 2 + 2
trial2_allele = ':'.join([_allele2[:3], _allele2[3:5], _allele2[5:7], _allele2[7:]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial2 = sr_TEMP.match(trial2_allele)
if Flag_trial2.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial2_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
elif len(_allele2) == 10:
# (1) 3 + 3 + 2 + 2
trial1_allele = ':'.join([_allele2[0:3], _allele2[3:6], _allele2[6:8], _allele2[8:10]]) + (_allele_Suffix if _allele_Suffix != -1 else "")
Flag_trial1 = sr_TEMP.match(trial1_allele)
if Flag_trial1.any():
[__RETURN__, LOG_MESSAGE] = get1stAllele2(trial1_allele, _d__HAT__, _from, _OUTPUT_FORMAT, __leave_NotFound, _allele0=_allele)
else:
__RETURN__ = _allele if __leave_NotFound else "0"
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
return [__RETURN__, LOG_MESSAGE]
def get1stAllele2(_allele, _df, _from, _OUTPUT_FORMAT, __leave_NotFound=False, _allele0=None):
__1st_Allele__ = None
LOG_MESSAGE = None
sr_from = _df[_from]
##### < HAT column to use (`_to`) > #####
if _OUTPUT_FORMAT == 0:
# Default mode. (`_from` == `_to`)
if _from == 'STANDARD':
_to = 1
elif _from == 'OLD':
_to = 1
elif _from == 'Ggroup':
_to = 3
elif _from == 'Pgroup':
_to = 4
else:
_to = -1
elif 0 < _OUTPUT_FORMAT <= 4:
_to = 1
elif _OUTPUT_FORMAT == 5:
_to = 3
elif _OUTPUT_FORMAT == 6:
_to = 4
else:
_to = -1
##### < Main Matching job > #####
## (1) Exact match
Flag_exact_match = sr_from.str.match(_allele + '$')
f_exact = False
if Flag_exact_match.any():
# (ex. '03:28' -> '03:28')
df_candidate = _df.loc[Flag_exact_match, :]
__1st_Allele__ = df_candidate.iat[0, _to]
f_exact = True
else:
## (2) Just match
Flag_match = sr_from.str.match(_allele)
if Flag_match.any():
# (ex. '03:28' -> '03:280')
df_candidate = _df.loc[Flag_match, :]
__1st_Allele__ = df_candidate.iat[0, _to]
else:
## (3) Nothing matched.
__1st_Allele__ = _allele if __leave_NotFound else '0'
if __leave_NotFound:
LOG_MESSAGE = '[Leave Not Found] {} -> {}'.format(_allele, _allele)
else:
LOG_MESSAGE = "[Not Found] {} -> 0".format(_allele)
return [__1st_Allele__, LOG_MESSAGE]
##### < Log message & Field trimming > #####
if _from == 'OLD':
if _to == 1:
if _OUTPUT_FORMAT == 4:
# to Standard
LOG_MESSAGE = "[{}] {} -> {}(OLD) => {}(STANDARD)".format(
'Exact match' if f_exact else 'Approximated', _allele, df_candidate.iat[0, 2], __1st_Allele__)
if not f_exact and df_candidate.shape[0] > 0:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(
df_candidate.iloc[:, [2, 1]].apply(' -> '.join, axis=1).tolist())])
else:
# 0 <= _OUTPUT_FORMAT < 4
__1st_Allele_cutted__ = FieldCutter(':'.join(a+b for a,b in zip(_allele0[::2], _allele0[1::2])), __1st_Allele__, _OUTPUT_FORMAT)
# to Standard
LOG_MESSAGE = "[{}] {} -> ({}(OLD) -> {}(STANDARD)) => {}".format(
'Exact match' if f_exact else 'Approximated', _allele, df_candidate.iat[0, 2], __1st_Allele__, __1st_Allele_cutted__)
if not f_exact and df_candidate.shape[0] > 0:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(
df_candidate.iloc[:, [2, 1]].apply(' -> '.join, axis=1).tolist())])
__1st_Allele__ = __1st_Allele_cutted__
elif _to == 3 or _to == 4:
# to Ggroup or Pgroup
LOG_MESSAGE = "[{}] {} -> ({}(OLD) -> {}(STANDARD)) => {}".format(
'Exact match' if f_exact else 'Approximated', _allele, df_candidate.iat[0, 2], df_candidate.iat[0, 1], __1st_Allele__)
if not f_exact and df_candidate.shape[0] > 0:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(
df_candidate.iloc[:, [2, 1, _to]].apply(' -> '.join, axis=1).tolist())])
elif _from == 'Ggroup':
s_temp = '({}'.format(_allele) if _allele0 == _allele else '{} -> ({}'.format(_allele0, _allele)
if _to == 1:
# There would be no duplicates in this case block.
f_exact_Ggroup = f_exact and (df_candidate.shape[0] == 1)
if _OUTPUT_FORMAT == 4:
# to Standard
LOG_MESSAGE = "[{}] {} => {}(STANDARD))".format(
'Exact match' if f_exact_Ggroup else 'Approximated', s_temp, __1st_Allele__)
if not f_exact_Ggroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(df_candidate.iloc[:, _to].tolist())])
else:
# 0 < _OUTPUT_FORMAT < 4
# the case "_OUTPUT_FORMAT == 0" can't be here. It will go to next "_to == 3" case block.
__1st_Allele_cutted__ = FieldCutter(_allele, __1st_Allele__, _OUTPUT_FORMAT)
LOG_MESSAGE = "[{}] {} -> {}(STANDARD)) => {}".format(
'Exact match' if f_exact_Ggroup else 'Approximated', s_temp, __1st_Allele__, __1st_Allele_cutted__)
if not f_exact_Ggroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(df_candidate.iloc[:, _to].tolist())])
__1st_Allele__ = __1st_Allele_cutted__
elif _to == 3:
# to G-group itself.
df_candidate = df_candidate.drop_duplicates(['Ggroup'])
# print(df_candidate)
f_exact_Ggroup = f_exact and (df_candidate.shape[0] == 1)
LOG_MESSAGE = "[{}] ({} => {})".format(
'Exact match' if f_exact_Ggroup else 'Approximated', _allele0, __1st_Allele__)
if not f_exact_Ggroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(df_candidate.iloc[:, _to].tolist())])
elif _to == 4:
# to Pgroup
df_candidate = df_candidate.drop_duplicates(['Ggroup', 'Pgroup'])
# print(df_candidate)
f_exact_Ggroup = f_exact and (df_candidate.shape[0] == 1)
LOG_MESSAGE = "[{}] {} => {})".format(
'Exact match' if f_exact else 'Approximated', s_temp, __1st_Allele__)
if not f_exact_Ggroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(
df_candidate.iloc[:, [3, _to]].apply(' -> '.join, axis=1).tolist())])
elif _from == 'Pgroup':
s_temp = '({}'.format(_allele) if _allele0 == _allele else '{} -> ({}'.format(_allele0, _allele)
if _to == 1:
f_exact_Pgroup = f_exact and (df_candidate.shape[0] == 1)
if _OUTPUT_FORMAT == 4:
# to Standard.
LOG_MESSAGE = "[{}] {} => {}(STANDARD))".format(
'Exact match' if f_exact_Pgroup else 'Approximated', s_temp, __1st_Allele__)
if not f_exact_Pgroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(df_candidate.iloc[:, _to].tolist())])
else:
# 0 < _OUTPUT_FORMAT < 4
# the case "_OUTPUT_FORMAT == 0" can't be here. It will go to next "_to == 4" case block.
__1st_Allele_cutted__ = FieldCutter(_allele, __1st_Allele__, _OUTPUT_FORMAT)
LOG_MESSAGE = "[{}] {} -> {}(STANDARD)) => {}".format(
'Exact match' if f_exact_Pgroup else 'Approximated', s_temp, __1st_Allele__, __1st_Allele_cutted__)
if not f_exact_Pgroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(df_candidate.iloc[:, _to].tolist())])
__1st_Allele__ = __1st_Allele_cutted__
elif _to == 3:
# to G-group
df_candidate = df_candidate.drop_duplicates(['Ggroup', 'Pgroup'])
f_exact_Pgroup = f_exact and (df_candidate.shape[0] == 1)
LOG_MESSAGE = "[{}] {} => {})".format(
'Exact match' if f_exact_Pgroup else 'Approximated', s_temp, __1st_Allele__)
if not f_exact_Pgroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(
df_candidate.iloc[:, [4, _to]].apply(' -> '.join, axis=1).tolist())])
elif _to == 4:
# to P-group itself.
df_candidate = df_candidate.drop_duplicates(['Pgroup'])
f_exact_Pgroup = f_exact and (df_candidate.shape[0] == 1)
LOG_MESSAGE = "[{}] ({} => {})".format(
'Exact match' if f_exact_Pgroup else 'Approximated', _allele0, __1st_Allele__)
if not f_exact_Pgroup:
LOG_MESSAGE = ' '.join([LOG_MESSAGE, "(Possible candidates: {})".format(df_candidate.iloc[:, _to].tolist())])
else:
if _to == 1:
if _OUTPUT_FORMAT == 4:
# to Standard
LOG_MESSAGE = "[{}] {} => {}(STANDARD)".format(
'Exact match' if f_exact else 'Approximated', _allele0 if bool(_allele0) else _allele, __1st_Allele__)