• 1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).
• 2 Prerequisites to run Python programs in Pymodule
  • 2.1 PyPi package: Palos
  • 2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3
  • 2.1.2 Build and upload the palos package to PyPi
  • 2.2 Optional prerequisites
  • 2.3 Optional C++ libraries
• 3 Example on how to run some pymodule programs

Yu S. Huang, [email protected]

1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).

This repository is a mix 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/ contains the source code of the https://pypi.org/project/palos module.

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

GADA/ contains a faster algorithm than the original GADA (2008/2009) by using a Red-Black tree. Now in an independent repo https://github.com/polyactis/eGADA.

ngs/ contains programs analyzing next-generation sequencing data.

2 Prerequisites to run Python programs in Pymodule

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

2.1 PyPi package: Palos

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

Install/Upgrade the Python3 version of Palos

pip3 install --upgrade palos

Install/Upgrade the Python2 version of Palos

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

2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3

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

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

2.1.2 Build and upload the palos package to PyPi

# Build the package.
# sdist and bdist_wheel are both commands of setup.py, not package names.
python3 setup.py sdist bdist_wheel

# (Delete old ones beforehand) and Upload the compiled package file.
# Enter your PyPi username (__token__) and password (!= the pypi.org account password).
twine upload dist/*

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