Biopython-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.68

Author / Distributor

Biopython

Description

"Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics." More details are at Biopython

Running Program

The last version of this application is at /usr/local/apps/eb/Biopython/1.68-foss-2016b-Python-2.7.14

To use this version, please load the module with

ml Biopython/1.68-foss-2016b-Python-2.7.14 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_Biopython
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Biopython.%j.out
#SBATCH --error=Biopython.%j.err

cd $SLURM_SUBMIT_DIR
ml Biopython/1.68-foss-2016b-Python-2.7.14
python [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml Biopython/1.68-foss-2016b-Python-2.7.14 
python -h
usage: python [option] ... [-c cmd | -m mod | file | -] [arg] ...
Options and arguments (and corresponding environment variables):
-b     : issue warnings about comparing bytearray with unicode
         (-bb: issue errors)
-B     : don't write .py[co] files on import; also PYTHONDONTWRITEBYTECODE=x
-c cmd : program passed in as string (terminates option list)
-d     : debug output from parser; also PYTHONDEBUG=x
-E     : ignore PYTHON* environment variables (such as PYTHONPATH)
-h     : print this help message and exit (also --help)
-i     : inspect interactively after running script; forces a prompt even
         if stdin does not appear to be a terminal; also PYTHONINSPECT=x
-m mod : run library module as a script (terminates option list)
-O     : optimize generated bytecode slightly; also PYTHONOPTIMIZE=x
-OO    : remove doc-strings in addition to the -O optimizations
-R     : use a pseudo-random salt to make hash() values of various types be
         unpredictable between separate invocations of the interpreter, as
         a defense against denial-of-service attacks
-Q arg : division options: -Qold (default), -Qwarn, -Qwarnall, -Qnew
-s     : don't add user site directory to sys.path; also PYTHONNOUSERSITE
-S     : don't imply 'import site' on initialization
-t     : issue warnings about inconsistent tab usage (-tt: issue errors)
-u     : unbuffered binary stdout and stderr; also PYTHONUNBUFFERED=x
         see man page for details on internal buffering relating to '-u'
-v     : verbose (trace import statements); also PYTHONVERBOSE=x
         can be supplied multiple times to increase verbosity
-V     : print the Python version number and exit (also --version)
-W arg : warning control; arg is action:message:category:module:lineno
         also PYTHONWARNINGS=arg
-x     : skip first line of source, allowing use of non-Unix forms of #!cmd
-3     : warn about Python 3.x incompatibilities that 2to3 cannot trivially fix
file   : program read from script file
-      : program read from stdin (default; interactive mode if a tty)
arg ...: arguments passed to program in sys.argv[1:]

Other environment variables:
PYTHONSTARTUP: file executed on interactive startup (no default)
PYTHONPATH   : ':'-separated list of directories prefixed to the
               default module search path.  The result is sys.path.
PYTHONHOME   : alternate <prefix> directory (or <prefix>:<exec_prefix>).
               The default module search path uses <prefix>/pythonX.X.
PYTHONCASEOK : ignore case in 'import' statements (Windows).
PYTHONIOENCODING: Encoding[:errors] used for stdin/stdout/stderr.
PYTHONHASHSEED: if this variable is set to 'random', the effect is the same
   as specifying the -R option: a random value is used to seed the hashes of
   str, bytes and datetime objects.  It can also be set to an integer
   in the range [0,4294967295] to get hash values with a predictable seed.

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Installation

Source code is obtained from Biopython

System

64-bit Linux