Misc Python modules developed and used by the yfish group
Project description
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.
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.
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}')
Optional prerequisites
The following pakcages are optional, only needed for some functions.
- python-mysqldb
- python-psycopg2 http://initd.org/psycopg/
- matplotlib basemap toolkit http://matplotlib.sourceforge.net/basemap/doc/html/
- python imaging library http://www.pythonware.com/products/pil/
- python-scientific http://www.scipy.org/
- biopython
- python-rpy
- networkx https://networkx.lanl.gov/wiki
- hcluster
- python-h5py
- python-tables
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
Example on how to run some pymodule programs
./ngs/DownsampleWorkflow.py -h
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