synthaser 1.0.1

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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:

$ pip install synthaser

or clone the repo and install locally:

$ 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:

$ synthaser -qi <accessions> OR synthaser -qf query.fasta

For example, performing a synthaser run on the cichorine PKS:

$ 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:

$ 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:

$ 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:

1. <pending>