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Tool for mapping homologous proteins

Project description

##Hyper Utility Tool Service (using protein ortholog tables)

  • Developer(s):
    • Cas Franciscus Martinus van Rijbroek (August 2019 - January 2020)
  • Version: 0.0
  • Release date: None

####What is HUTSpot?

HUTSpot is a python application developed for HAN Biocentre. It aims to create a reliable mapping of homologous proteins between organisms to facilitate research projects. Because the application is developed for HAN Biocentre, all software is designed to work with local resources running at there. Feel free to adjust the configurations of the project to work with your own resources.

####How do I obtain HUTSpot?

HUTSpot is an open source project hosted at [GitLab](https://zero.han.nl/gitlab/Cas.vanRijbroek/hutspot).

####Configuration

A config.json file is included in the resources folder of the main hutspot package contained within the source code. All static paths and options are defined there as a JSON object. Keep in mind that all values need to be inserted as strings. Clarification on the contents:

  • accepted_orgs: a nested list of organism definitions. A single organism consists of 3 items:
    • The full scientific name of the organism.
    • An abbreviation of the name for the g:profiler.
    • The ncbi taxonomic ID of the organism.
    • Example: [“Homo sapiens”, “hsapiens”, “9606”].
  • elasticsearch: data related to the configuration of the elasticsearch, contains 2 items:
    • host: IP address of the database.
    • port: Port that the database communicates through.
  • hutspotdb: data related to the configuration of the HUTSpot MongoDB, contains the following items:
    • host: IP address of the database.
    • port: Port that the database communicates through.
    • username: Username for the user of the database.
    • password: Password for the user of the database.
    • database_name: Name for the HUTSpot database.
    • pathway_collection: Name for the pathways collection.
    • status_collection: Name for the job status collection.
    • alignment_collection: Name for the alignments collection.
    • error_log_collection: Name for the error log collection.

####How can I use it?

Currently only the back-end of the application has been completed. The application can be run from the command line as a non-interactive program. The script can also be imported and used by other python applications.

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