Metadata-Version: 1.1
Name: proScatter
Version: 0.0.1
Summary: for visualizing pLink data from one or more experiments
Home-page: https://github.com/justinjee/proScatter
Author: Justin Jee
Author-email: justin.jee@gmail.com
License: MIT
Description: proScatter
        ==========
        
        For visualizing pLink data from one or more experiments
        -------------------------------------------------------
        
        by Katelyn McGary Shipper, Justin Jee, and Ilya Shamovsky
        
        *Dependencies*
        
        proScatter uses `python <https://www.python.org/downloads/>`__,
        `numpy <http://www.numpy.org/>`__,
        `bokeh <http://bokeh.pydata.org/en/latest/index.html>`__, and
        `pandas <http://pandas.pydata.org/>`__
        
        *Basic Use*
        
        To download, either download all 3 .py files into the same directory, or
        download the zipped folder (see button on the bottom right)
        
        The inputs to proScatter include:
        
        1. A fasta file including the amino acid sequences of all the proteins
           under consideration.
        2. A list of amino acids of interest (ex: K or CM)
        3. pLink output in ``.html`` format
        
        The outputs include:
        
        1. A summary file (.txt) containing the list of all links and their
           frequencies
        2. A scatter plot
        
        *Example*
        
        ``./proScatter.py examples/test.fasta examples/IdProTable_combine.html``
        
        Features
        --------
        
        proScatter enables multiple features, for example:
        
        ``python proScatter.py test.fasta K test.html --scale --zoom=Prot1-Prot2 --evalue=0.001``
        
        Details are given below:
        
        *--scale*
        
        Scales both plot and output so that only the amino acids of interest are
        considered. Axes are in units of amino acids of interest (ex: 1st
        lysine, 2nd lysine, etc)
        
        *--zoom=Prot1-Prot2*
        
        Zooms in on only one subplot (Prot1 vs Prot2). As an added feature,
        clicking on any point in the scatter plot will print the coordinates of
        that point in the console.
        
        *--evalue=#*
        
        Considers only links with a score below a certain number #. Scores are
        expected to be in the 5th column
        
        ::
        
                 usage: proScatter.py [-h] [-a AMINOACIDS] [-z ZOOM] [-s] [-e EVALUE] [-u]
                                      [-o OUTPUT] [-v]
                                      fasta_file plink
                 
                 positional arguments:
                   fasta_file            fasta file with protein sequences
                   plink                 pLink output .html file
                 
                 optional arguments:
                   -h, --help            show this help message and exit
                   -a AMINOACIDS, --aminoacids AMINOACIDS
                                         cross-linkable aminoacids. Defaults to Lysine (K).
                   -z ZOOM, --zoom ZOOM  Prot1-Prot2 only display subplot for proteins Prot1 vs
                                         Prot2
                   -s, --scale           scale both plot and outputs so that only amino acids
                                         of interest are considered
                   -e EVALUE, --evalue EVALUE
                                         e-value cutoff
                   -u, --unjoin          unjoin plot axes
                   -o OUTPUT, --output OUTPUT
                                         output file (HTML) name
                   -v, --verbose         increase output verbosity
        
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
