expam 0.0.1

Metagenomic profiling using a reference phylogeny

 
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Contents

Install.

• From PyPI.
• From GitLab source.

Tutorials.

FAQ

Commands.

Bug Reports.

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Install.

From Bioconda (Recommended)

From PyPI

user@computer:~$ pip install expam

From GitLab source

To install from source, you need a local installation of Python >=3.8, as well as numpy and cython. There are some commonly encountered problems when installing on Linux, the most common of which are outlined in the FAQ section below.

First download the source code from the GitLab repository.

user@computer:~$ git clone [e-mail]:ssol0002/pam.git

This can then be installed locally by executing the following command from the source code root:

user@computer:~$ python3 setup.py install

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Documentation

Documentation

An outline of all available commands and flags is can be found in the /docs/ folder.

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Tutorials

0. Setting up a conda environment (optional)

Link - setting up the conda environment and installing expam dependencies.

1. Basics tutorial

Link - building a database and classifying reads.

2. Classification output in-depth

Link - organising sample classifications, and displaying results.

3. Building a tree

Link - create a distance tree to be used for building the database.

4. Visualising results

Link - depicting classification results on a phylotree.

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FAQ

Problems during installation

error: g++: Command not found

This is simply a matter of updating the compiler.

> sudo apt-get install build-essential

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fatal error: Python.h: No such file or directory

This simply means you need to install/update the Python development files for version 3.

> sudo apt-get install python3-dev

(Reference - SO)

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ete3 importing errors

For instance, ImportError: cannot import name 'NodeStyle'.

The ete3 module depends on Qt, and for Linux it may take some tweaking to get Python to recognise the local installation of Qt. The following seems to work for a broad collection of circumstances.

First update the local installation of Qt.

> sudo apt-get install qt5-default

Now double-check which version of Qt has been installed.

> dpkl -l | grep "pyqt5"

Install the corresponding Python interface to Qt.

> pip3 install pyqt5==5.12

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Commands

Flag	Input	Description
-h/--help	N/A	Print help command.
-db/--db_name	diretory	Path to database directory (relative or absolute).
-k/--k	integer	K-value for analysis.
-n/--n	integer	Number of processes spawned when building database and classifying read. Number of threads passed to mashtree in mashtree command.
-p/--phylogeny	directory	Path to phylogeny/Newick file.
-d/--directory	directory	Path to directory.
-y/--pile	integer	Number of genomes to pile when making database. Leave as default if you don't want to mess with the natural order.
--first	integer	Add first [value] genomes from some directory into the database.

A complete list of available commands can by found by using the -h/--help flags.

user@computer:~$ expam --help
...

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Bug Reports

Please raise any bug reports at https://gitlab.erc.monash.edu.au/ssol0002/pam/-/issues accompanied by any error messages, a rough description of the database/setup and parameters used to create the database.