Soumya

candl_tmp.csv

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+1,ABL1,T,212,R,9,133738234,ACG,uc004bzw.3,+,634,4,AGG,Chronic Myelocytic Leukemia,3,20519627
+2,ABL1,T,212,R,9,133738235,ACG,uc004bzw.3,+,635,4,AGG,Chronic Myelocytic Leukemia,3,20519627
+2769,AKT1,,0,,14,0,,,,0,0,,Lung,3,
+32,AKT1,E,17,K,14,105246550,GAG,uc001ypn.3,-,50,3,AAG,Lung,4,"17611497, 23134728"
+157,ARAF,F,351,L,x,47426806,TTC,uc011mlp.3,+,1051,10,TTG,Langerhans Cell Histiocytosis,3,24652991
+2767,BRAF,,0,,7,0,,,,0,0,,"Colon, Astrocytoma",4,

csvrecords.py

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+import csv
+
+txt_file = r"allAnnotatedVariants.txt"
+csv_file = r"mycsv.csv"
+
+in_txt = csv.reader(open(txt_file, "rb"), delimiter = '\t')
+out_csv = csv.writer(open(csv_file, 'wb'))
+
+out_csv.writerows(in_txt)

dataonco.py

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+import csv
+import pymysql
+pymysql.install_as_MySQLdb()
+import MySQLdb
+from urllib.request import urlretrieve
+import os
+
+
+url = "http://oncokb.org/api/v1/utils/allAnnotatedVariants.txt"
+urlretrieve(url,"oncotxt.txt")
+
+with open('oncotxt.txt', 'r') as infile, open('oncocsv.csv', 'w') as outfile:
+    in_txt = csv.reader(infile, delimiter = '\t')
+
+    out_csv = csv.writer(outfile)
+    out_csv.writerows(in_txt)
+'''with open("test.csv",'r') as f:
+    with open("oncocsv.csv",'w') as f1:
+        next(f) # skip header line
+        for line in f:
+            f1.write(line)'''
+
+os.remove('oncotxt.txt')
+
+def MapOncokb(d):
+    d['Database'] = 'OncoKB'
+    d['Mutation'] = 0
+    d['Signature'] = 1
+    d['Variant'] = 99999
+    d['Functionality'] = 3
+    d['Impact'] = 99999
+    d['Indication'] = 99999
+    d['Domain'] = 99999
+    d['Classification'] = 99999
+    d['Reference'] = 4
+
+    return d
+
+def MapFunctionality(str):
+    functionality = { # OncoKB map
+         'Loss-of-function': 'LOF', 'Likely Loss-of-function': 'LOF',
+         'Gain-of-function': 'GOF', 'Likely Gain-of-function': 'GOF',         
+         'Switch-of-function': 'SOF', 'Likely Switch-of-function': 'SOF',         
+         'Mutation Effect': 'COF', 'Likely Mutation Effect': 'COF',         
+         'Inconclusive':  'Inconclusive',
+         'Neutral':  'Neutral', 'Likely Neutral':  'Neutral', 'null': 'NA',
+         # 
+
+         }
+
+    return functionality[str.strip()]
+
+
+def WriteDB(dbFd, dbMap, row):
+
+    tblRow = 10*['NA']
+
+    tblRow[0] = dbMap['Database']
+    tblRow[1] = row [dbMap['Mutation']]
+    tblRow[2] =  row [dbMap['Signature']]
+    if (dbMap['Variant'] != 99999):
+        tblRow[3] = (row [dbMap['Variant']])
+    if (dbMap['Functionality'] != 99999):
+        tblRow[4] =  MapFunctionality (row [dbMap['Functionality']])
+    if (dbMap['Impact'] != 99999):
+        tblRow[5] = row [dbMap['Impact']]
+    if (dbMap['Indication'] != 99999):
+        tblRow[6] = row [dbMap['Indication']]
+    if (dbMap['Domain'] != 99999):
+        tblRow[7] = row [dbMap['Domain']]
+    if (dbMap['Classification'] != 99999):
+        tblRow[8] = row [dbMap['Classification']]
+    if (dbMap['Reference'] != 99999):
+        tblRow[9] = row [dbMap['Reference']]
+
+    return tblRow    
+
+dbFd = 1
+
+myfile = open('finalrecord.csv', 'w')
+writer = csv.writer(myfile, delimiter=',')
+
+oncoMap = dict()
+MapOncokb(oncoMap)
+
+
+with open('oncocsv.csv', 'r') as csvFd: 
+    reader = csv.reader(csvFd, delimiter=',')
+    next(reader)
+    for row in reader:              
+        lin = WriteDB(dbFd, oncoMap, row)
+        writer.writerow(lin)
+os.remove('oncocsv.csv')
+
+
+database = MySQLdb.connect(host='localhost', user='root', passwd='root')
+cursor = database.cursor()
+create_database = "CREATE DATABASE IF NOT EXISTS cellworksDATA"
+cursor.execute(create_database)
+database = MySQLdb.connect(host='localhost', user='root', passwd='root', db='cellworksDATA')
+cursor = database.cursor()
+create_table = "CREATE TABLE IF NOT EXISTS cellworksTABLE (Data VARCHAR(255), Mutation VARCHAR(255), Signature VARCHAR(255), Variant VARCHAR(255), Functionality VARCHAR(255), Impact VARCHAR(255), Indication VARCHAR(255), Domain VARCHAR(255), Classification VARCHAR(255), Reference VARCHAR(255))"
+cursor.execute(create_table)
+with open('finalrecord.csv', "r") as file:
+ reader = csv.reader(file)
+ for row in reader:
+    if len(row) == 10:
+        cursor.execute('INSERT INTO cellworksTABLE (Data,Mutation,Signature,Variant,Functionality,Impact,Indication,Domain,Classification,Reference) VALUES("%s","%s","%s","%s","%s","%s","%s","%s","%s","%s")', (row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7], row[8], row[9]))
+    else:
+        print('Error in row: ')
+        print(row)
+database.commit()
+cursor.close()
+
+os.remove('finalrecord.csv')

dataonco.py~

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+import csv
+import pymysql
+pymysql.install_as_MySQLdb()
+import MySQLdb
+from urllib.request import urlretrieve
+import os
+
+
+url = "http://oncokb.org/api/v1/utils/allAnnotatedVariants.txt"
+urlretrieve(url,"oncotxt.txt")
+
+with open('oncotxt.txt', 'r') as infile, open('oncocsv.csv', 'w') as outfile:
+    in_txt = csv.reader(infile, delimiter = '\t')
+
+    out_csv = csv.writer(outfile)
+    out_csv.writerows(in_txt)
+'''with open("test.csv",'r') as f:
+    with open("oncocsv.csv",'w') as f1:
+        next(f) # skip header line
+        for line in f:
+            f1.write(line)'''
+
+os.remove('oncotxt.txt')
+
+def MapOncokb(d):
+    d['Database'] = 'OncoKB'
+    d['Mutation'] = 0
+    d['Signature'] = 1
+    d['Variant'] = 99999
+    d['Functionality'] = 3
+    d['Impact'] = 99999
+    d['Indication'] = 99999
+    d['Domain'] = 99999
+    d['Classification'] = 99999
+    d['Reference'] = 4
+
+    return d
+
+def MapFunctionality(str):
+    functionality = { # OncoKB map
+         'Loss-of-function': 'LOF', 'Likely Loss-of-function': 'LOF',
+         'Gain-of-function': 'GOF', 'Likely Gain-of-function': 'GOF',         
+         'Switch-of-function': 'SOF', 'Likely Switch-of-function': 'SOF',         
+         'Mutation Effect': 'COF', 'Likely Mutation Effect': 'COF',         
+         'Inconclusive':  'Inconclusive',
+         'Neutral':  'Neutral', 'Likely Neutral':  'Neutral', 'null': 'NA',
+         # 
+
+         }
+
+    return functionality[str.strip()]
+
+
+def WriteDB(dbFd, dbMap, row):
+
+    tblRow = 10*['NA']
+
+    tblRow[0] = dbMap['Database']
+    tblRow[1] = row [dbMap['Mutation']]
+    tblRow[2] =  row [dbMap['Signature']]
+    if (dbMap['Variant'] != 99999):
+        tblRow[3] = (row [dbMap['Variant']])
+    if (dbMap['Functionality'] != 99999):
+        tblRow[4] =  MapFunctionality (row [dbMap['Functionality']])
+    if (dbMap['Impact'] != 99999):
+        tblRow[5] = row [dbMap['Impact']]
+    if (dbMap['Indication'] != 99999):
+        tblRow[6] = row [dbMap['Indication']]
+    if (dbMap['Domain'] != 99999):
+        tblRow[7] = row [dbMap['Domain']]
+    if (dbMap['Classification'] != 99999):
+        tblRow[8] = row [dbMap['Classification']]
+    if (dbMap['Reference'] != 99999):
+        tblRow[9] = row [dbMap['Reference']]
+
+    return tblRow    
+
+dbFd = 1
+
+myfile = open('finalrecord.csv', 'w')
+writer = csv.writer(myfile, delimiter=',')
+
+oncoMap = dict()
+MapOncokb(oncoMap)
+
+
+with open('oncocsv.csv', 'r') as csvFd: 
+    reader = csv.reader(csvFd, delimiter=',')
+    next(reader)
+    for row in reader:              
+        lin = WriteDB(dbFd, oncoMap, row)
+        writer.writerow(lin)
+os.remove('oncocsv.csv')
+
+
+
+database = MySQLdb.connect(host='localhost', user='root', passwd='root')
+cursor = database.cursor()
+create_database = "CREATE DATABASE IF NOT EXISTS cellworksDATA"
+cursor.execute(create_database)
+database = MySQLdb.connect(host='localhost', user='root', passwd='root', db='cellworksDATA')
+cursor = database.cursor()
+create_table = "CREATE TABLE IF NOT EXISTS cellworksTABLE (Data VARCHAR(255), Mutation VARCHAR(255), Signature VARCHAR(255), Variant VARCHAR(255), Functionality VARCHAR(255), Impact VARCHAR(255), Indication VARCHAR(255), Domain VARCHAR(255), Classification VARCHAR(255), Reference VARCHAR(255))"
+cursor.execute(create_table)
+with open('finalrecord.csv', "r") as file:
+ reader = csv.reader(file)
+ for row in reader:
+    if len(row) == 10:
+        cursor.execute('INSERT INTO cellworksTABLE (Data,Mutation,Signature,Variant,Functionality,Impact,Indication,Domain,Classification,Reference) VALUES("%s","%s","%s","%s","%s","%s","%s","%s","%s","%s")', (row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7], row[8], row[9]))
+    else:
+        print('Error in row: ')
+        print(row)
+database.commit()
+cursor.close()
+
+os.remove('finalrecord.csv')

dataonco2.py

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+import csv
+import MySQLdb
+from urllib import urlretrieve
+import os
+
+
+url = "http://oncokb.org/api/v1/utils/allAnnotatedVariants.txt"
+urlretrieve(url,"oncotxt.txt")
+
+with open('oncotxt.txt', 'r') as infile, open('oncocsv.csv', 'w') as outfile:
+    in_txt = csv.reader(infile, delimiter = '\t')
+
+    out_csv = csv.writer(outfile)
+    out_csv.writerows(in_txt)
+'''with open("test.csv",'r') as f:
+    with open("oncocsv.csv",'w') as f1:
+        next(f) # skip header line
+        for line in f:
+            f1.write(line)'''
+
+os.remove('oncotxt.txt')
+
+def MapOncokb(d):
+    d['Database'] = 'OncoKB'
+    d['Mutation'] = 0
+    d['Signature'] = 1
+    d['Variant'] = 99999
+    d['Functionality'] = 3
+    d['Impact'] = 99999
+    d['Indication'] = 99999
+    d['Domain'] = 99999
+    d['Classification'] = 99999
+    d['Reference'] = 4
+
+    return d
+
+def MapFunctionality(str):
+    functionality = { # OncoKB map
+         'Loss-of-function': 'LOF', 'Likely Loss-of-function': 'LOF',
+         'Gain-of-function': 'GOF', 'Likely Gain-of-function': 'GOF',         
+         'Switch-of-function': 'SOF', 'Likely Switch-of-function': 'SOF',         
+         'Mutation Effect': 'COF', 'Likely Mutation Effect': 'COF',         
+         'Inconclusive':  'Inconclusive',
+         'Neutral':  'Neutral', 'Likely Neutral':  'Neutral', 'null': 'NA',
+         # 
+
+         }
+
+    return functionality[str.strip()]
+
+
+def WriteDB(dbFd, dbMap, row):
+
+    tblRow = 10*['NA']
+
+    tblRow[0] = dbMap['Database']
+    tblRow[1] = row [dbMap['Mutation']]
+    tblRow[2] =  row [dbMap['Signature']]
+    if (dbMap['Variant'] != 99999):
+        tblRow[3] = (row [dbMap['Variant']])
+    if (dbMap['Functionality'] != 99999):
+        tblRow[4] =  MapFunctionality (row [dbMap['Functionality']])
+    if (dbMap['Impact'] != 99999):
+        tblRow[5] = row [dbMap['Impact']]
+    if (dbMap['Indication'] != 99999):
+        tblRow[6] = row [dbMap['Indication']]
+    if (dbMap['Domain'] != 99999):
+        tblRow[7] = row [dbMap['Domain']]
+    if (dbMap['Classification'] != 99999):
+        tblRow[8] = row [dbMap['Classification']]
+    if (dbMap['Reference'] != 99999):
+        tblRow[9] = row [dbMap['Reference']]
+
+    return tblRow    
+
+dbFd = 1
+
+myfile = open('finalrecord.csv', 'w')
+writer = csv.writer(myfile, delimiter=',')
+
+oncoMap = dict()
+MapOncokb(oncoMap)
+
+
+with open('oncocsv.csv', 'r') as csvFd: 
+    reader = csv.reader(csvFd, delimiter=',')
+    next(reader)
+    for row in reader:              
+        lin = WriteDB(dbFd, oncoMap, row)
+        writer.writerow(lin)
+#os.remove('oncocsv.csv')
+
+
+database = MySQLdb.connect(host='localhost', user='root', passwd='root')
+cursor = database.cursor()
+create_database = "CREATE DATABASE IF NOT EXISTS cellworksDATA"
+cursor.execute(create_database)
+database = MySQLdb.connect(host='localhost', user='root', passwd='root', db='cellworksDATA')
+cursor = database.cursor()
+create_table = "CREATE TABLE IF NOT EXISTS cellworksTABLE (Data VARCHAR(255), Mutation VARCHAR(255), Signature VARCHAR(255), Variant VARCHAR(255), Functionality VARCHAR(255), Impact VARCHAR(255), Indication VARCHAR(255), Domain VARCHAR(255), Classification VARCHAR(255), Reference VARCHAR(255))"
+cursor.execute(create_table)
+with open('finalrecord.csv', "r") as file:
+ reader = csv.reader(file)
+ for row in reader:
+    if len(row) == 10:
+        cursor.execute('INSERT INTO cellworksTABLE (Data,Mutation,Signature,Variant,Functionality,Impact,Indication,Domain,Classification,Reference) VALUES("%s","%s","%s","%s","%s","%s","%s","%s","%s","%s")', (row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7], row[8], row[9]))
+    else:
+        print('Error in row: ')
+        print(row)
+database.commit()
+cursor.close()
+
+os.remove('finalrecord.csv')