Command Line Interface

This page will introduce you to iPhylo CLI (Command-Line Interface), a simple tool for automatically generating biological and chemical taxonomic trees based on species names, taxID or chemical identifiers, or any customized tree generated from data you define!

The command-line usage is well-suited for professional users, which includes and expands upon all the features of the iPhylo web version. The localization and command line usage makes it faster and easier to run on a cluster of computers.

Download code ZIP:

Github: https://github.com/ARise-fox/iPhylo-CLI/

Environment: The iPhylo command line is a program written in python, make sure you have Python 3 installed and configured before you start working with it.

Packages: You will need to install some necessary packages before you can run it correctly, which can be done quickly with the following pip commands.

pip install -r requirements.txt

Phylotree

This module is used to generate a phylogenetic tree of organisms, run the following command for help:

python iphylo.py phylotree -h

Use the following commands to start your try:


                                
python iphylo.py phylotree -i "Homo sapiens,Mus musculus,Gallus gallus,Drosophila melanogaster,Escherichia coli" 

                                
python iphylo.py phylotree -i 9606,10090,9031,7227,562

Chemtree

This module is used to generate a taxonomic tree of chemicals, run the following command for help:

python iphylo.py chemtree -h

Use the following commands to have some try:


                                
python iphylo.py chemtree -f 'example/inchikeys.txt' -fn 'chem_01'

Chem Online

This module is an extension of the chemtree module, which allows you to query compounds categorized outside of the local database, and requires a network connection for its use.

Run the following command for help:

python iphylo.py chemonline -h

Use the following commands to have some try:


                                
python  iphylo.py chemonline -f 'example/inchikeys_for_online.txt' -fn 'chem_02'

CSV2Tree

You can use this module to build a tree for any data with a hierarchy.

The data should be presented in a csv table, with each row representing a categorized piece of information and each column representing a categorization level.

Here is an example of statistical analysis methods:

Statistical Analysis Hypothesis Tests Parametric Tests One Sample t test
Statistical Analysis Hypothesis Tests Parametric Tests One Sample z test
Statistical Analysis Hypothesis Tests Parametric Tests Two Samples Independent Samples Two-group t test
Statistical Analysis Hypothesis Tests Parametric Tests Two Samples Independent Samples z test
Statistical Analysis Hypothesis Tests Nonparametric Tests One Samples Kolmogorov-Smirnov
Statistical Analysis Hypothesis Tests Nonparametric Tests One Samples Binomial
Statistical Analysis Hypothesis Tests Nonparametric Tests Two Samples Paired Samples Wilcoxon
Statistical Analysis Hypothesis Tests Nonparametric Tests Two Samples Paired Samples Chi-square

Use the following command for more help information:

python iphylo.py csv2tree --help