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synthaser parses the results of a batch NCBI conserved domain search and determines
the domain architecture of secondary metabolite synthases.
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 .
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.
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
$ synthaser -qi CBF69451.1 \ --cdsid QM3-qcdsearch-14C5BC063AA03DDE-15B11AB00918AED0 \ --svg figure.svg
The generated figure is then saved in
figure.svg, and looks like:
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 (
For example, searching PKS sequences from A. nidulans:
$ synthaser -qf sequences.fasta --json nidulans.svg
synthaser --help for all tweakable parameters for generating the SVG.
If you found
synthaser helpful, please cite:
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