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Project description
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>
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