pyCHiC

This repository contains pipelines for analyzing capture Hi-C data. CHiCAGO algorithm is used for the normalization of chromatin contacts

Requirements

• pyenv and pyenv-virtualenv

• Python 3.6

• Python Modules:

  • pylint
  • pytest
  • mg-tool-api
  • rpy2
  • matplotlib==2.2.3
  • pandas==0.23.4
  • rtree
  • rpy2
  • numpy==1.14.5
  • pandas
  • scipy==1.1.0
  • multiprocess
  • matplotlib

• R >=3.1.2 -R Modules: -argparser -survival -Hmisc -devtools -Chicago

• bedtools

• perl

• spatialindex

• bowtie2

• hicup

Installation

For a guide to the full installation procedure the see ReadTheDocs.

Directly from GitHub:

.. code-block:: none :linenos:

cd ${HOME}/code

git clone https://github.com/Multiscale-Genomics/pyCHiC.git

cd CHi-C

Create the Python environment

.. code-block:: none :linenos:

pyenv-virtualenv 2.7.10 CHi-C pip install --editable .

Tests

Tests must be runned from the top directory. Test for single tools are runned with pytest, example: $pytest tests/test_rmap_tool.py There is an order to run single tests:

• test_rmap_tool.py
• test_baitmap.py
• test_design.py
• test_hicup.py
• test_bam2chicago.py
• test_pyCHiC.py

To run all test type: $python tests/test_toolchains.py

IMPORTANT! From the top directory type ./tidy_data before running tests/test_toolchains.py

To test run_pyCHiC_pipeline: python run_pyCHiC_pipeline.py --bowtie_idx tests/data/test_baitmap/chr21_hg19.fa.bt2.tar.gz --genome_fa tests/data/test_baitmap/chr21_hg19.fa --probes_fa tests/data/test_baitmap/h19_promoter.fa --fastq1 tests/data/test_truncater/SRR3535023_1_chr21_new.fastq --fastq2 tests/data/test_truncater/SRR3535023_2_chr21_new.fastq --execution . --RE_name HindIII --RE_sequence A^AGCTT --execution test_run --minNPerBait 1 --minProxOEPerBin 1 --minProxB2BPerBin 1 --techNoise_minBaitsPerBin 1 --cutoff 1

Command Line

pyCHiC/run_pyCHiC_pipeline.py is a command line tool to run the complete CHiC pipeline. Use python run_pyCHiC_pipeline.py -h for more information.

pyCHiC/CHiC/tool/cline_pyCHiC.py are command line tools to tun the pyCHiC tool. Use python cline_pyCHiC.py -h for more information.