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Misc Python modules developed and used by the yfish group

Project description

1. A repo that contains miscellaneous Python programs and a 'palos' module by the yfish group.

This repository is mixture of a python module 'palos' and other standalone programs developed and used by the yfish group, http://www.yfish.org/.

It contains code related to bioinformatics projects focusing on next-generation sequencing data, population genetics, genome-wide association studies, pedigree genetics, etc.

palos/ is the source of the https://pypi.org/project/palos module.

palos/algorithm/ contains pure algorithms, not specific to Bioinformatics.

GADA/ contains a fast segmentation algorithm/program. It contains some bugfixes and improvement over the original GADA (2008/2009) by using a Red-Black tree to accelerate its speed.

ngs/ contains programs analyzing next-generation sequencing data.

2. Prerequisites to run Python programs in Pymodule

Most programs in pymodule is dependent on the palos module, which is housed in palos/. Installation of palos will trigger installation of other dependencies.

2.1. Palos

Palos supports Python3 primarily, but is ported to Python2 via https://github.com/asottile/future-fstrings, because some pymodule programs are Python2-only.

pip3 install --upgrade palos
# to run some Python2 pymodule programs
pip install --upgrade palos

Package future-fstrings allows the use of f-string in Python2.

# -*- coding: future_fstrings -*-
thing = 'world'
print(f'hello {thing}')

2.2. Optional prerequisites

The following pakcages are optional, only needed for some functions.

  1. mysqldb
  2. biopython
  3. pegaflow https://pypi.org/project/Pegaflow/
  4. psycopg2 http://initd.org/psycopg/
  5. matplotlib basemap toolkit http://matplotlib.sourceforge.net/basemap/doc/html/
  6. python imaging library http://www.pythonware.com/products/pil/
  7. python-scientific http://www.scipy.org/
  8. biopython
  9. python-rpy2
  10. networkx https://networkx.lanl.gov/wiki
  11. hcluster
  12. python-h5py
  13. python-tables

2.3. Optional C++ libraries

Required if you plan to compile all binaries in pymodule by typeing 'make all'.

apt-get install libhdf5-dev libhdf5-serial-dev libhdf5-cpp-100 hdf5-tools
libarmadillo-dev libboost-program-options-dev libboost-iostreams-dev
libboost-python-dev python-dev

3. Example on how to run some pymodule programs

./ngs/DownsampleWorkflow.py  -h

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