example_tb-profiler-webdriver_script.py

###################
#### Create DB ####
###################

# This is just a simple in-memory sqlite database for this example.
# It will obviously not be necessary in your case as you already created the database.

from sqlalchemy import Table, Column, Integer, String, MetaData, ForeignKey
from sqlalchemy import create_engine

engine = create_engine('sqlite:///:memory:', echo=True)

metadata = MetaData()

patient_mutations = Table('patient_genes_mutations', metadata,
    Column('id', Integer, primary_key=True),
    Column('mut_id', Integer),
    Column('patient_id', Integer),
)

unique_mutations =  Table('unqiue_mutations', metadata,
    Column('id', Integer, primary_key=True),
    Column('mutation', String),
    Column('gene_id', String),
)


patients =  Table('patients', metadata,
    Column('id', Integer, primary_key=True),
)

metadata.create_all(engine)


###########################
#### Using tb-profiler ####
###########################

# Here we use download an example fastq file and upload it to TB-Profiler webserver using the driver

import tbprofiler_webdriver
import urllib
from time import sleep
# Get an example file
urllib.request.urlretrieve("http://bioinformatics.lshtm.ac.uk/static/por5A_min.fastq.gz", "por5A_min.fastq.gz")


# Create server object (default: host="https://localhost:5000")
server = tbprofiler_webdriver.tbprofiler_server(host="http://bioinformatics.lshtm.ac.uk")

# Send fastq files to be processed (default: platform="illumina")
run_id = server.send_fastq("por5A_min.fastq.gz")

# Retrieve results
result = server.get_result(run_id)
while result["status"]!="OK":
    result = server.get_result(run_id)
    print("Result not ready yet... Waiting 5 seconds.")
    sleep(5)


###########################
##### Insert into DB ######
###########################

# This is an example of how you can commit the results to your database

from sqlalchemy.sql import select

# Patient ID is defined by process
patient_id = "12345"

conn = engine.connect()

for var in result["result"]["dr_variants"]:
    # Test if mutation exists already in unique_mutations table
    if conn.execute("SELECT * FROM unqiue_mutations WHERE mutation=? and gene_id=?", var["change"], var["locus_tag"]).first()==None:
        conn.execute(unique_mutations.insert(), mutation=var["change"], gene_id=var["locus_tag"])

    # Get mutaion ID
    mutation_id = conn.execute("SELECT * FROM unqiue_mutations WHERE mutation=? and gene_id=?", var["change"], var["locus_tag"]).first()[0]

    # Add Mutation -> Patient rows
    conn.execute(patient_mutations.insert(), mut_id=mutation_id, patient_id=patient_id)


# Check table contents
for row in conn.execute(select([unique_mutations])):
    print(dict(row))

for row in conn.execute(select([patient_mutations])):
    print(dict(row))