Metadata-Version: 2.1
Name: Palos
Version: 0.1.35
Summary: Misc Python modules developed and used by the yfish group
Home-page: https://github.com/polyactis/pymodule
Author: Yu S. Huang
Author-email: polyactis@gmail.com
License: Apache2
Description: - [1 A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).](#1-a-repo-that-contains-miscellaneous-pythonc-modulesprograms-a-standalone-python-module-palos-by-the-yfish-group-can-be-installed-by-pip)
        - [2 Prerequisites to run Python programs in Pymodule](#2-prerequisites-to-run-python-programs-in-pymodule)
          - [2.1 PyPi package: Palos](#21-pypi-package-palos)
          - [2.1.1 Package future-fstrings ensures compatibility between Python2 and Python3](#211-package-future-fstrings-ensures-compatibility-between-python2-and-python3)
          - [2.1.2 Build and upload the palos package to PyPi](#212-build-and-upload-the-palos-package-to-pypi)
          - [2.2 Optional prerequisites](#22-optional-prerequisites)
          - [2.3 Optional C++ libraries](#23-optional-c-libraries)
        - [3 Example on how to run some pymodule programs](#3-example-on-how-to-run-some-pymodule-programs)
        
        Yu S. Huang, polyactis@gmail.com
        
        # 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/](palos/) contains the source code 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 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/](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/](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
        ```sh
        pip3 install --upgrade palos
        ```
        
        
        Install/Upgrade the Python2 version of Palos
        ```sh
        # 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.
        ```python
        # -*- coding: future_fstrings -*-
        thing = 'world'
        print(f'hello {thing}')
        ```
        
        ## 2.1.2 Build and upload the palos package to PyPi
        
        ```bash
        # 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
        
        ```sh
        ./ngs/DownsampleWorkflow.py  -h
        ```
        
        
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Utilities
Requires-Python: >=2.7
Description-Content-Type: text/markdown
