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Misc Python modules developed and used by the yfish group

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# 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 to run Python programs in Pymodule Most programs in pymodule is dependent on the palos module, which is housed in [palos/](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.

`sh pip3 install --upgrade palos `

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

Package future-fstrings allows the use of f-string in Python2. `python # -*- coding: future_fstrings -*- thing = 'world' print(f'hello {thing}') `

## Optional prerequisites

The 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

# Example on how to run some pymodule programs

`sh ./ngs/DownsampleWorkflow.py  -h `

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