<commit_before>Installation
------------------

1. Clone the repository:

        git clone <EMAIL>:jordiabante/nucleosome_positioning.git 

2. Add the bin folder in the repository to your path variable by adding the following line to the `.bashrc` (`.bash_profile` in Mac) file:

        export PATH="path/to/bin:$PATH"

3. If the machine running the code is Machintosh install coreutils (sudo port install coreutils) as well as: sed, gzip, grep, getopt, mysql, openssl, readline, boost, zlib. Add the following line to the `.bashrc` (`.bash_profile` in Mac) file:

        export PATH="/opt/local/bin:$PATH"
        export PATH="/opt/local/libexec/gnubin:$PATH"

Dependancies
-----------------
1. samtools

Usage
-----------------

1. Every folder (`script_name`) will contain the following files and directories:
  1. `sript_name.sh`: bash script
  2. `main/`
    * `main.sh`: bash script to try the command with toy example.
    * Files required for the toy example.

![stormtroop](https://octodex.github.com/images/stormtroopocat.png)
<commit_msg>Added HTSeq<commit_after>Installation
------------------

1. Clone the repository:

        git clone <EMAIL>:jordiabante/nucleosome_positioning.git 

2. Add the bin folder in the repository to your path variable by adding the following line to the `.bashrc` (`.bash_profile` in Mac) file:

        export PATH="path/to/bin:$PATH"

3. If the machine running the code is Machintosh install coreutils (sudo port install coreutils) as well as: sed, gzip, grep, getopt, mysql, openssl, readline, boost, zlib. Add the following line to the `.bashrc` (`.bash_profile` in Mac) file:

        export PATH="/opt/local/bin:$PATH"
        export PATH="/opt/local/libexec/gnubin:$PATH"

Dependancies
-----------------
1. samtools
2. HTSeq

Usage
-----------------

1. Every folder (`script_name`) will contain the following files and directories:
  1. `sript_name.sh`: bash script
  2. `main/`
    * `main.sh`: bash script to try the command with toy example.
    * Files required for the toy example.

![stormtroop](https://octodex.github.com/images/stormtroopocat.png)

{'fraction_non_alphanumeric': 0.14732354334438655, 'fraction_numerical': 0.0071056371387967785, 'mean_word_length': 3.0075901328273247, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 2, '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': '4274324', 'n_tokens_mistral': 682, 'n_tokens_neox': 625, 'n_words': 231}