This program can be directly installed from github. (green code button, top right)
Due to the software versions of python and the application's dependencies, creating a conda enviroment will be most useful.
If you have conda skip, otherwise refer to online resources on how to install conda.
Once installed, we can make a conda environment
conda create -n population_genetics
conda activate population_genetics
change directories into created NCBI_Taxon_Genome_Link-master directory
cd NCBI_Taxon_Genome_Link-master
The python version for running this script is python=3.9.9
conda install python=3.9.9
The script runs with python depencies, lxml==4.8.0 and urllib3==1.26.8.
If not already installed, they can be isntalled as such.
pip install lxml==4.8.0
pip install urllib3==1.26.8
The script should be all ready to run.
The code can be run as follows
python NCBI_Taxon_Genome_link.py [-h] [-v] [-s] -e EMAIL -i USER_INPUT [USER_INPUT ...] [-o OUTPUT]
The help page can be accessed with the -h or --help flag
python NCBI_Taxon_Genome_link.py -h
python NCBI_Taxon_Genome_link.py --help
The program version can be accessed with the -v or --version flag
python NCBI_Taxon_Genome_link.py -v
python NCBI_Taxon_Genome_link.py --version
There are two required fields for running NCBI_Taxon_Genome_link.py, EMAIL and USER_INPUT. Email is required for accessing NCBI's databases remotely. USER_INPUT is your taxon/TaxID of interest. Both can be typed out directly on the terminal.
python NCBI_Taxon_Genome_link.py -e EMAIL -i USER_INPUT
There are two optional fields, SUB_SPECIES and OUTPUT.
The SUB_SPECIES tag does not take any input.
python NCBI_Taxon_Genome_link.py -e EMAIL -i USER_INPUT -s
The OUTPUT tag takes a desired output file name
python NCBI_Taxon_Genome_link.py -e EMAIL -i USER_INPUT -o assembled_genomes.txt
Various ways of searching for humans.
With scientific species name.
python NCBI_Taxon_Genome_link.py -e researcher@fake_email.com -i Homo sapiens
With TaxID.
python NCBI_Taxon_Genome_link.py -e researcher@fake_email.com -i 9606
With common name.
python NCBI_Taxon_Genome_link.py -e researcher@fake_email.com -i human
With taxonomic rank family.
python NCBI_Taxon_Genome_link.py -e researcher@fake_email.com -i Hominidae
The number of assembled genomes are printed directly out to the standard output. However, specifying the output flag, prints the species and assembled genomes to an output file.
an example output for Homo sapiens without outputfile.
python NCBI_Taxon_Genome_link.py -e researcher@fake_email.com -i Homo sapiens
#Homo sapiens is of rank species
#found 0 children taxon
#number of assembled genomes for Homo sapiens is 1220
an example output for Homo sapiens with outputfile.
python NCBI_Taxon_Genome_link.py -e researcher@fake_email.com -i Homo sapiens -o example_outputfile.txt
#Homo sapiens is of rank species
#found 0 children taxon
#number of assembled genomes for Homo sapiens is 1220
refer to example_outputfile.txt in folder for format.