Metadata-Version: 2.1
Name: synthaser
Version: 1.1.7
Summary: UNKNOWN
Home-page: https://github.com/gamcil/synthaser
Author: Cameron Gilchrist
License: UNKNOWN
Description: # synthaser
        [![Coverage Status](https://coveralls.io/repos/github/gamcil/synthaser/badge.svg?branch=master)](https://coveralls.io/github/gamcil/synthaser?branch=master&service=github)
        [![Documentation Status](https://readthedocs.org/projects/synthaser/badge/?version=latest)](https://synthaser.readthedocs.io/en/latest/?badge=latest)
        [![PyPI version](https://badge.fury.io/py/synthaser.svg)](https://badge.fury.io/py/synthaser)
        
        ## Process
        `synthaser` parses the results of a batch NCBI conserved domain search and determines
        the domain architecture of secondary metabolite synthases.
        
        ## Installation
        Install from PyPI using pip:
        
        ```sh
        $ pip install --user synthaser
        ```
        
        or clone the repo and install locally:
        
        ```sh
        $ git clone https://www.github.com/gamcil/synthaser
        $ cd synthaser
        $ pip install -e .
        ```
        
        ## Dependencies
        `synthaser` is written for Python 3.6+ and its only external Python dependency is
        `requests`, which is used for querying the NCBI's APIs. To perform local
        searches, the programs `RPS-BLAST` as well as the CD-Search post-processing
        utility, `rpsbproc`, should be installed (available from ...)
        
        ## Usage
        A full `synthaser` search can be performed as simply as:
        
        ```sh
        $ synthaser -qf sequences.fasta
        ```
        
        Where `sequences.fasta` is a FASTA format file containing the protein sequences
        that you would like to search.
        
        For a full listing of available arguments, enter:
        
        ```sh
        $ synthaser -h
        ```
        
        ### Visualising your results
        `synthaser` is capable of generating fully-interactive, annotated visualisations
        so you can easily explore your results. All that is required is one
        extra argument:
        
        ```sh
        $ synthaser -qf sequences.fasta -p
        ```
        
        This will generate a figure like so:
        
        <img src="./img/anid_pks.png"
        	width="400"
        	alt="Example synthaser output">
        
        Click here to play around with the full version of this example.
        
        ### Saving your search session
        `synthaser` allows you to save your search results such that they can be easily
        reloaded for further visualisation or exploration without having to fully re-do
        the search.
        
        To do this, use the `--json_file` command:
        
        ```sh
        $ synthaser -qf sequences.fasta --json_file sequences.json
        ```
        
        This will save all of your results, in JSON format, to the file
        `sequences.json`. Then, loading this session back into `synthaser`, is as easy
        as:
        
        ```sh
        $ synthaser --json_file sequences.json ...
        ```
        
        ### Using your own rules
        Though `synthaser` was originally designed to analyse secondary metabolite synthases,
        it can easily be repurposed to analyse the domain architectures of
        any type of protein sequence.
        
        Under the hood, `synthaser` uses two files to determine 1) which domains to save
        from a CD-Search run (`domains.json`) and 2) the rules used to classify sequences based on their
        domain architectures (`rules.json`). By default, `synthaser` will use the copies
        of these files distributed with the program. However, providing your own rules
        is as simple as:
        
        ```sh
        $ synthaser -qf sequences.fasta -df my_domains.json -cf my_rules.json
        ```
        
        For a detailed explanation of how to create your own `synthaser` rule files,
        as well as API 
        please refer to the `documentation`.
        
        ## Citations
        If you found `synthaser` helpful, please cite:
        
        ```sh
        1. <pending>
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
