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/](palos/) is the source of the [https://pypi.org/project/palos](https://pypi.org/project/palos) module.
[palos/algorithm/](palos/algorithm/) contains pure algorithms, not specific to Bioinformatics.
[GADA/](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/](ngs/) contains programs analyzing next-generation sequencing data.
# Prerequisites The palos module is universally used by many programs and must be installed before running any program in pymodule.
## Optional prerequisites
Following pakcages are optional, only needed for some functions.
1. python-mysqldb 1. python-psycopg2 http://initd.org/psycopg/ 1. matplotlib basemap toolkit http://matplotlib.sourceforge.net/basemap/doc/html/ 1. python imaging library http://www.pythonware.com/products/pil/ 1. python-scientific http://www.scipy.org/ 1. biopython 1. python-rpy 1. networkx https://networkx.lanl.gov/wiki 1. hcluster 1. python-h5py 1. 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
## Install palos
`sh pip3 install --upgrade palos `
# Usage
`sh ./ngs/DownsampleWorkflow.py -h `
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.