ccb-sb/plsdbapi

API for the plasmid database PLSDB

PLSDB is a resource of plasmid records that are collected from the NCBI database and subsequently processed to remove incomplete, inconsistent or chromosomal entries, and to add annotations. This package allows to connect to the PLSDB webserver and download plasmid data. Hence, a stable internet connection is required. To find out more about PLSDB please visit our web server.

All PLSDB tools are provided and hosted by the Chair for Clinical Bioinformatics at Saarland University.

Data accessible with plsdbapi

• general data about one or more plasmids using the NCBI accession id: query_plasmid_id
• search nucleotide sequences in PLSDB with mash screen, mash dist, blastn and tblastn: query_plasmid_sequence
• filter PLSDB according to e.g. name, location or length and download the found plasmids: query_plasmid_filter
• fasta sequences can be downloaded with query_plasmid_id and query_plasmid_filter as well as with download_fasta

To see some examples on how to use plsdbapi in python and R read the quickstart guides.

 

Installation

Python package

git clone [email protected]:CCB-SB/plsdbapi.git
cd plsdbapi
pip install .

 

Conda

conda install -c ccb-sb plsdbapi

plsdbapi's Issues

i wonder how long does it take for the web server to be fully maintained?

i wonder how long does it take for the web server to be fully maintained?

error: Query sequence with mash_screen

In Linux, a Python script was invoked, and upon executing the command, it displayed the following message: "Http response is not OK. Response status code is 502."

I would really appreciate if you could explain me what's going on here.

Thanks a lot!

I wonder if this dataset still needs to undergo preprocessing steps such as quality control, redundancy removal, and pruning?

I wonder if this dataset still needs to undergo preprocessing steps such as quality control, redundancy removal, and pruning?