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This file contains instructions on running NGS Python example programs.

Once installed, the source code is contained in *.py files. Each source file corresponds to a separate example that demonstrates use of a particular feature of the NGS Python API.

To be run, the examples require python3 installed and in PATH. See 4) below for a way to override.

In order to run Python examples, the NGS package needs to be installed. To install, run the following commands:
    cd <path-to-sra-tools>/ngs/ngs-python
    python3 setup.py install --user
<path-to-sra-tools> should point to the root of the root directory of the source checkout (not the installation location)

1. Run all
    - run "make". This will run all examples with their predefined arguments. The output of all the examples goes to stdout.

2. Run and diff
    - run "make run_and_diff". This will execute all the examples with their predefined arguments, run them, capture the output in a temporary file, and then use "diff" to compare the actual output against a file containing the expected output (./expected.txt). Any discrepancies will be displayed. If the actual output matches the expected, there will be a message "NGS Python examples work as expected" at the end of the execution.

3. Run separately
    - run "make <example>" where <example> is one of "run_frag", "run_align", "run_align_slice", "run_pileup", "run_ref". This will run the selected example with some predefined arguments.
    - In order to run an individual example with custom arguments, do so using Python from the command line, e.g.
        python3 AlignTest ERR225922 10000 2
    - When run without arguments, the examples will output a very short description of the required parameters.

4. Alternative Python Interpreter
    - By default, the makefile invokes Python as "python3".
    - To change that, specify makefile variable PYTHON to point to an alternative path to the Python interpreter, e.g. "make PYTHON=/usr/bin/python"
    - Note that the examples will not work using versions of Python older than 3.6.