#Import webscraper json how to#
#Import webscraper json install#
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cazy_webscraper can be installed from the command-line with: conda install cazy_webscraper The latest version of cazy_webscraper is guarenteed to be installed via bioconda. If you have the bioconda channel available. Installing via bioconda (Quick and easy installation)Д¬azy_webscraper is available in the bioconda channel of conda. There are three different methods to install cazy_webscraper: The python libraries listed within requirements.txt Installation All feedback is greatly appreciated and the aim is provide a tool users will find extremely useful! Requirements If there any additional features you would like to see added to cazy_webscraper or the documentation, please do raise an issue in the GitHub repo. This will likely be slow in development but it will come in the next 6-9 months. To make cazy_webscraper accessible to a wider audience, I will (after the release of version 1) add on a GUI for cazy_webscraper. However, we are working on developing written and video tutorials to help users will less experience using the cmd-line to get started with this tool!ДЄll this work is being done on the currently active update_expand branch. Progress on the Expand module: Retrieving sequences for specific classes and families from a dictionary created using cazy_webscraper is complete, although no unit tests have been written yet.Дocumentation: The ReadTheDocs documentation has been updated to include all cmd-line flag.

#Import webscraper json code#

The code will be factorised out into multiple submodules, and include allow applying an additional EC number filter for selecting CAZyme to retrieve structural and sequence data for. The Expand module: This module is for retrieving protein sequences from GenBank and PDB structures from PDB. Unit Tests: The coverage of the unit tests will be increased to cover at least 95% of the entire package We're almost at the stage of releasing the first version of cazy_webscraper, but there are a few things we want to do first. Our last developments before releasing version 1! (2021): cazy_webscraper Microbiology Society Annual Conference 2021 poster.

Pritchard, Leighton Chapman, Sean Gloster, Tracey M. This is not only helpful for us as developers to get out work out into the world, but it is also essential for the reproducibility and integrity of scientific research.Д¬itation: Hobbs, Emma E. If you use cazy_webscraper in your work please do cite our work (including the provided DOI), as well as citing the specific version you use. It is expected academic practise to cite the work of others.

Retrieve the PDB accessions of all CAZymes derived from all strains of Escherichia coli, whcih are annotated with at least of the EC numbers EC3.2.1.23, EC3.2.1.25 and are from the CAZy families GH2 and/or GH5.

Retrieve the GenBank accessions of CAZymes from GT2, derived from Aspergillus or Trichoderma species, and have a PDB structure file accession.

Retrieve the GenBank accessions of all CAZymes derived from all Aspergillus species.

Retrieve the PDB accessions of all CAZymes present in GH1 and/or GH3.

Retrieve the names of all organisms with at last CAZyme in PL1 and at least one CAZymes in AA2.

Use cazy_webscraper to create a local SQL database, then using SQL perform complex queries against the dataset which cannot be performed on the CAZy website. In slower time we hope to supplementary these with videos as well, for the visual learnersД¬azy_webscraper can be installed both via bioconda channel of conda, and via Pypi ( pip) for quick and easy installation.Д¬AZyme database for thorough interogation of the data

#Import webscraper json how to#

If you are new to bioinformatics and/or installing/using command-line tools, we've written a series of step-by-step instructions on how to install and use cazy_webscraper, which you can find here.

#Import webscraper json full#

An additional taxonomy filter can be applied to restrict the scraping of CAZymes to specific Kingdoms, genera, species and/or strains.ДЇor detailed documentation see the full documentation.ДЄn ER model can be found in the root of the cazy_webscraper GitHub repo, demonstrating the structure of the SQL database create by cazy_webscraper. The program additionally, includes an expand module, which can retrieve the protein sequences from GenBank and protein structure files from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB).Д¬azy_webscraper can be configured to scrape the entire database, selected Classes and/or selected CAZy families.

#Import webscraper json license#

This program is free to use under the MIT license when proper recognition is given.Д¬azy_webscraper retrieves protein data from CAZy, producing a local SQL database which enables uses to throughly interrogate the data in a manner unachievable through the CAZy website. Cazy_webscraper is a Python3 package for the automated retrieval of protein data from the CAZy database.