<commit_before>fastqp
======

simple NGS read quality assessment using Python

Requirements
------------
Python 2.7
    - matplotlib
    
Installation
------------
`python setup.py install`
    
Usage
-----

    usage: fastqp [-h] [-v] [-s SAMPLE] [-k {2,3,4,5,6,7,8,9,10}] [-o OUTPUT] [-f]
                  [--nokmer]
                  input
    
    simple NGS read quality assessment using Python
    
    positional arguments:
      input                 input file (FASTQ or SAM)
    
    optional arguments:
      -h, --help            show this help message and exit
      -v, --verbose         verbose output
      -s SAMPLE, --sample SAMPLE
                            number of reads to sample from
      -k {2,3,4,5,6,7,8,9,10}, --kmer {2,3,4,5,6,7,8,9,10}
                            length of kmer for over-repesented kmer counts
      -o OUTPUT, --output OUTPUT
                            base name for output files
      -f, --figures         produce figures
      --nokmer              do not count kmers
      
Examples
--------

![quality percentiles](https://raw.github.com/mdshw5/fastqp/master/examples/example_quals.png)
<commit_msg>update install instructions<commit_after>fastqp
======

simple NGS read quality assessment using Python

Requirements
------------
Python 2.7
    - numpy
    - matplotlib
Tested on Mac OS 10.8 and Linux 2.6.18
    
Installation
------------
`sudo pip install numpy matplotlib`
`wget https://github.com/mdshw5/fastqp/archive/fastqp-0.1.tar.gz`
`tar -xvzf fastqp-0.1.tar.gz`
`cd fastqp-0.1`
`sudo python setup.py install`
    
Usage
-----

    usage: fastqp [-h] [-v] [-s SAMPLE] [-k {2,3,4,5,6,7,8,9,10}] [-o OUTPUT] [-f]
                  [--nokmer]
                  input
    
    simple NGS read quality assessment using Python
    
    positional arguments:
      input                 input file (FASTQ or SAM)
    
    optional arguments:
      -h, --help            show this help message and exit
      -v, --verbose         verbose output
      -s SAMPLE, --sample SAMPLE
                            number of reads to sample from
      -k {2,3,4,5,6,7,8,9,10}, --kmer {2,3,4,5,6,7,8,9,10}
                            length of kmer for over-repesented kmer counts
      -o OUTPUT, --output OUTPUT
                            base name for output files
      -f, --figures         produce figures
      --nokmer              do not count kmers
      
Examples
--------

![quality percentiles](https://raw.github.com/mdshw5/fastqp/master/examples/example_quals.png)

{'fraction_non_alphanumeric': 0.13162055335968378, 'fraction_numerical': 0.03162055335968379, 'mean_word_length': 1.5721544715447155, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 3, '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': '1476812', 'n_tokens_mistral': 822, 'n_tokens_neox': 783, 'n_words': 226}