chenyyxx/EQTL

Python Program (Library) to calculate linear regression between gene expression and gene synapse

EQTL

Python Program (Library) to calculate linear regression between gene expression and gene synapse

Dependencies

statsmodels, pyvcf, mysql-connector-python, scikit-learn, pandas, pysam

Before Running: please install the following libraries

pip install --upgrade --no-deps statsmodels

pip install PyVCF

pip install mysql-connector-python

pip install scikit-learn

pip install pandas

pip install pysam

Data

The Data file should be put into the Data folder

Acceptible data format: synpase .vcf, .txt, .vcf.gz

gene expression .txt

Important notes

• Please put the tabix index file for vcf: .vcf.gz.tbi inside the same directory.
• The name prefix of the tabix index file should be exactly same with the vcf file.

Input

• User will nee to specify four input:
  1. synapse name (id)
  2. gene expression name
  3. synapse vcf data path
  4. gene expression data path
• User will specify their input by modifying the user_input.csv inside the user_input folder.

TODO

1. Optimize the indexing of gene expression file (currently use a map for indexing, higher space complexity).
2. Make sure the result is correcct when using real data to test
3. Handle more exceptions and corner cases.