Python IMGTdbIO.load_pickle2dict示例

示例#1

@author: hhuang2
"""

# import glob
import sqlite3 as sql
# from utils import phase_block_check as ps
from utils import IMGTdbIO, CompareSeq
import os
import re

locus = 'DQB1'

#pkl_fp = '../Output/SG39_DRpairs/SG39_HLA_'+ locus +'_paired.pkl'
pkl_fp = '../Output/SG39/2018/SG39_DRpairs/SG39_HLA_' + locus + '_paired.pkl'

DRpair_seqInfo = IMGTdbIO.load_pickle2dict(pkl_fp)

case_count = len(DRpair_seqInfo)
print('Locus ' + locus + ' has ' + str(case_count) + ' paired cases.')

DB_fp = "../Output/SG39/2018/SG39_DRpairs/SG39_HLA_" + locus + "_paired.db"
conn = sql.connect(DB_fp)
cursor = conn.cursor()
cursor.execute('''CREATE TABLE IF NOT EXISTS DR_pair_comparison 
               (BMT_caseID text, QC text, 
               PS1_HLATyping text, 
               PS1_GLstringM text, PS1_SeqM text, 
               PS2_HLATyping text,
               PS2_GLstringM text, PS2_SeqM text,
               Audit text, Active text, Comment text)''')

示例#2

文件： DR_comparison_stats_SG41_52.py 项目： hhuang2018/HLAWholeGeneAnalysis

"""
Created on Tue Oct  3 14:42:06 2017

@author: hhuang2
"""

import glob
import sqlite3 as sql
# from utils import phase_block_check as ps
from utils import IMGTdbIO, CompareSeq
import os
import re


fname = '../Output/SG41_52/2018/IMGTv3310/SG41_52_DRpair_Stats/SG41_52_pairedCases_Stats.pkl'
Matching_cases_stats = IMGTdbIO.load_pickle2dict(fname)

## 'All_paired'
groupType = 'fiveLoci_paired' # groupType = 'ClassI_paired' # groupType = 'All_paired'
group_caseIDs = Matching_cases_stats[groupType]
All_loci = ['A', 'B', 'C', 'DRB1', 'DQB1']#, 'DPB1']
ClassI_loci = ['A', 'B', 'C']
ClassII_loci = ['DRB1', 'DQB1']

CaseStats = {}
LocusStats = {}
#MatchStats = {}
for caseID in group_caseIDs:
    # 
    for locus in ClassI_loci:
        ARSregion = ['Exon2', 'Exon3']

示例#3

import glob
import csv

from utils import IMGTdbIO, CompareSeq


groupType = 'fiveLoci_paired' # groupType = 'ClassI_paired' # groupType = 'All_paired' ; 'fiveLoci_paired'

All_loci = ['A', 'B', 'C', 'DRB1', 'DQB1', 'DPB1']
Five_loci = ['A', 'B', 'C', 'DRB1', 'DQB1']
ClassI_loci = ['A', 'B', 'C']
ClassII_loci = ['DRB1', 'DQB1', 'DPB1']

Group_fname = '../Output/SG41_52/2018/IMGTv3310/SG41_52_DRpair_Stats/fiveLoci_paired_Stats_0125_' + groupType + '.pkl'
Stats_Dict = IMGTdbIO.load_pickle2dict(Group_fname)

CaseStats = Stats_Dict['CaseStats']
LocusStats = Stats_Dict['LocusStats']

db_fp= '../Database/'
#key = '83687'
#CaseStats[key] 
#key in group_caseIDs
## : paired cases HLA typing stats
fname = '../Output/SG41_52/2018/IMGTv3310/SG41_52_DRpair_Stats/SG41_52_pairedCases_Stats.pkl'
Matching_cases_stats = IMGTdbIO.load_pickle2dict(fname)

group_caseIDs = Matching_cases_stats[groupType]

CaseMatchTable = {}

示例#4

"""

import glob
import csv

from utils import IMGTdbIO, CompareSeq

groupType = 'fiveLoci_paired'  # groupType = 'ClassI_paired' # groupType = 'All_paired' ; 'fiveLoci_paired'

All_loci = ['A', 'B', 'C', 'DRB1', 'DQB1', 'DPB1']
Five_loci = ['A', 'B', 'C', 'DRB1', 'DQB1']
ClassI_loci = ['A', 'B', 'C']
ClassII_loci = ['DRB1', 'DQB1', 'DPB1']

Group_fname = '../Output/SG39/2018/SG39_Stats/fiveLoci_paired_Stats_0125_' + groupType + '.pkl'
Stats_Dict = IMGTdbIO.load_pickle2dict(Group_fname)

CaseStats = Stats_Dict['CaseStats']
LocusStats = Stats_Dict['LocusStats']

db_fp = '../Database/'
#key = '84571'
#CaseStats[key]
#key in group_caseIDs

## : paired cases HLA typing stats
fname = '../Output/SG39/2018/SG39_DRpairs/SG39_pairedCases_Stats.pkl'
Matching_cases_stats = IMGTdbIO.load_pickle2dict(fname)

CaseMatchTable = {}
for locus in All_loci:

示例#5

@author: hhuang2
"""

from utils import IMGTdbIO  #, CompareSeq
from collections import Counter

groupType = 'All_paired'  # groupType = 'ClassI_paired' # groupType = 'All_paired'

All_loci = ['A', 'B', 'C', 'DRB1', 'DQB1', 'DPB1']
Five_loci = ['A', 'B', 'C', 'DRB1', 'DQB1']
ClassI_loci = ['A', 'B', 'C']
ClassII_loci = ['DRB1', 'DQB1', 'DPB1']

Group_fname = '../Output/Stats/ClassI_Stats_1003_' + groupType + '.pkl'
Stats_Dict = IMGTdbIO.load_pickle2dict(Group_fname)

CaseStats = Stats_Dict['CaseStats']
LocusStats = Stats_Dict['LocusStats']

## TODO1: paired cases HLA typing stats
fname = '../Output/SG39_DRpairs/SG39_pairedCases_Stats.pkl'
Matching_cases_stats = IMGTdbIO.load_pickle2dict(fname)

AlleleStats = {}
for locus in All_loci:
    AlleleStats[locus] = {}
    DRpaired_file = '../Output/SG39_DRpairs/SG39_HLA_' + locus + '_paired.pkl'

    DRpaired_table = IMGTdbIO.load_pickle2dict(DRpaired_file)
    num_total = len(DRpaired_table)