Metadata-Version: 2.1
Name: synthaser
Version: 1.0.5
Summary: UNKNOWN
Home-page: https://github.com/gamcil/synthaser
Author: Cameron Gilchrist
License: UNKNOWN
Description: # synthaser
        [![Build Status](https://travis-ci.org/gamcil/synthaser.svg?branch=master)](https://travis-ci.org/gamcil/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 via pip:
        ```sh
        $ pip install 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 has been tested on Linux (Ubuntu 18.04) and
        Windows (10). The only external Python dependency is `requests`, which is used for
        querying the NCBI's APIs.
        
        ## Usage
        A search can be launched as simply as:
        ```sh
        $ synthaser -qi <accessions> OR synthaser -qf query.fasta
        ```
        
        For example, performing a `synthaser` run on the cichorine PKS:
        ```sh
        $ synthaser -qi CBF69451.1
        [11:13:42] INFO - Starting synthaser
        [11:13:44] INFO - Launching new CDSearch run on IDs: ['CBF69451.1']
        [11:13:45] INFO - Run ID: QM3-qcdsearch-14C5BC063AA03DDE-15B11AB00918AED0
        [11:13:45] INFO - Polling NCBI for results...
        [11:13:45] INFO - Checking search status...
        [11:14:05] INFO - Checking search status...
        [11:14:06] INFO - Search successfully completed!
        NR-PKS
        ------
        CBF69451.1      SAT-KS-AT-PT-ACP-ACP-MT-TE
        [11:14:06] INFO - Finished synthaser
        ```
        
        `synthaser` can also produce an SVG representation of the query synthases. For example,
        we could take the CDSID (CD-Search ID) of the previous run, and provide the `--svg` flag:
        
        ```sh
        $ synthaser -qi CBF69451.1 \
            --cdsid QM3-qcdsearch-14C5BC063AA03DDE-15B11AB00918AED0 \
            --svg figure.svg
        ```
        
        The generated figure is then saved in `figure.svg`, and looks like:
        
        <img
          src="https://raw.githubusercontent.com/gamcil/synthaser/master/img/cichorine_svg.png"
          width="600">
        
        `synthaser` can also start batch searches, either by providing more than one sequence in
        a query FASTA file (`-qf`), or more than one NCBI accession (`-qi`).
        
        For example, searching PKS sequences from *A. nidulans*:
        
        ```sh
        $ synthaser -qf sequences.fasta --json nidulans.svg
        ```
        
        Produces:
        
        <img
          src="https://raw.githubusercontent.com/gamcil/synthaser/master/img/anid_pks.png"
          width="600">
        
        Refer to `synthaser --help` for all tweakable parameters for generating the SVG.
        
        ## 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
