vDirect 0.0.7

Description:

vDirect 0.0.7

VDirect
VDirect is a user friendly tool to retrieve information from the VOGDB-API. It is a utility that builds URLs and sends requests to the server.
Functionality includes searching for species, proteins and virus orthologous groups (VOGs) objects, as well as getting more detailed information about these objects.
Fetching Multiple Sequence Alignments (MSA) and Hidden Markov Matrices (HMM) is possible for each VOG, and Aminoacid and Nucleotide Sequences can be fetched for proteins.
Dependencies:
You can install the dependencies with
pip install argparse
pip install requests

Installation
vDirect can be installed with:
pip install vDirect

Using the VOGDB-API with vDirect
Below is the search hierarchy: first specify vsearch, vsummary or vfetch, then the subsequent parameters.
'-h' provides a list of the parameters that can be used for filtering.
vdirect <base_url> vsearch species species_search_parameters
protein protein_search_parameters
vog vog_search_parameters

vsummary species species_ids
protein protein_ids
vog vog_ids

vfetch protein faa protein_ids
fna protein_ids
vog hmm vog_ids
msa vog_ids

Examples
vdirect http://127.0.0.1:8000/ vsearch vog -pmax 10 -pmin 10
vdirect http://127.0.0.1:8000/ vsearch species -n corona
vdirect http://127.0.0.1:8000/ vsearch protein -n corona
vdirect http://127.0.0.1:8000/ vfetch protein faa -id 1034149.YP_009198699.1

You can get summaries from the IDs returned by a search by using the shell syntax:
vdirect http://127.0.0.1:8000/ vsummary vog -id $(vdirect -base http://127.0.0.1:8000/ vsearch vog -pmax 100 -pmin 100)

You can also set the base url as an environment variable with
base='http://127.0.0.1:8000/'

and then execute the command as
vdirect $base vsummary vog -id $(vdirect $base vsearch vog -pmax 100 -pmin 100)

Authors
Nikola Vinko*, Sigi Koizar*
*University of Vienna