<commit_before>Installing AmpliconSoftClipper
==================
AmpliconSoftClipper has been tested with Python 2.7 on OSX and \*nix.

Prerequisites
-------------
.. note:: Pip installs all required libraries; see [Installing] below.


* natsort (3.5.2)  
* nosetests, testfixtures required for running automated tests


Installing
----------
You can install from source from github:

``$ pip install git+https://github.com/umich-brcf-bioinf/AmpliconSoftClipper``

If you don't have root permissions, you can install locally:

``$ pip install git+https://github.com/umich-brcf-bioinf/AmpliconSoftClipper --user``

Following the pip install, you may need to adjust your path settings to include home/.local/bin. 


If you already have pysam installed, you can also clone from github and run directly from the source like so:

``$ git clone https://github.com/umich-brcf-bioinf/AmpliconSoftClipper``

``$ AmpliconSoftClipper/clipper-runner.py manifest.txt input.bam output.bam``
  <commit_msg>Fixed INSTALL<commit_after>Installing AmpliconSoftClipper
==================
AmpliconSoftClipper has been tested with Python 2.7 on OSX and \*nix.

Prerequisites
-------------
.. note:: Pip installs all required libraries; see [Installing] below.


* natsort (3.5.2)  
* nosetests, testfixtures required for running automated tests


Installing
----------
You can install from source from github:

``$ pip install git+https://github.com/umich-brcf-bioinf/AmpliconSoftClipper``

If you don't have root permissions, you can install locally:

``$ pip install git+https://github.com/umich-brcf-bioinf/AmpliconSoftClipper --user``

Following the pip install, you may need to adjust your path settings to include home/.local/bin. 
Then you can execute so:

``$ clipper manifest.txt input.bam output.bam``

If you already have prerequisite modules installed, you can also clone from github and run directly from the source like so:

``$ git clone https://github.com/umich-brcf-bioinf/AmpliconSoftClipper``

``$ AmpliconSoftClipper/clipper-runner.py manifest.txt input.bam output.bam``
  
{'fraction_non_alphanumeric': 0.1278957528957529, 'fraction_numerical': 0.004826254826254826, 'mean_word_length': 4.208542713567839, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4278082', 'n_tokens_mistral': 644, 'n_tokens_neox': 616, 'n_words': 209}