Programs

This folder contains all scripts from this project. This folder also contains a folder with all the data files that are needed to run these scripts.

Deliverable 1

This deliverable parses a bed file and creates a dictionary that contains the bed file data.

Usage:

python3 deliverable1.py

Deliverable 2

This script parses and filters the pileup data form a pileup file and creates a coverage dictionary

Usage:

python3 deliverable2.py

Deliverable 3

This script reads a bed file, a pileup file and a coverage dictionary to calculate the coverage and writes this to a output file.

Usage:

python3 deliverable3.py

Deliverable 4

This script is the combination of deliverable 1, 2 and 3.
When run this script parses a bed file and the pileup file, creates a coverage dictionary and writes the coverage dictionary to an output file.

Usage:

python3 deliverable4.py bed_file pileup_file

Deliverable 5

This script reads a vcf file, checks each line if the frequency is above the threshold if this is true the line will be writen to the output vcf file.

Usage:

python3 deliverable5.py vcf_file min_frequency vcf_output_file

Deliverable 6

This script parses an ANNOVAR file and creates a list where each entery is a line of the ANNOVAR file as a dictionary.

Usage:

python3 delivarable6.py

Deliverable 7

This script reads the raw gene_names colomn from the ANNOVAR file and reformat's the name so only the gene name remains.

Usage:

python3 deliverable7.py

Deliverable 8

This file contains the code to create the database tables we need to fill in deliverable 9.

This file creates three tables:

• chromosomes
• genes
• variants

Usage:

mysql -u user -h host -D database - p < deliverable8.sql

or

mysqlsh -u user -h host -D database - p < deliverable8.sql

Deliverable 9

This script will connect to your database and add the data from a ANNOVAR file to the database.

Usage:

python3 deliverable9.py [-s sql_file] username password hostname database_name annovar_file