changwanseo / funid

Fungal Identification Pipeline

This is Beta release. Bug reports are welcomed

Scheduling

Beta release part 1 (2023 Feburary ~ As paper published, ver 0.3)

• Will be tested by our lab memebers to fix bugs and advance features

Beta release part 2 (As paper published ~ When pipeline gets stabled, ver 0.4)

• Will be tested by peer taxonomists

Stable release (ver 1.0)

FunVIP

"Fun"gal "V"alidation & "I"dentification "P"ipeline

An automatic tree-based sequence identification and validation pipeline for fungal species

• Automatic tree-based identification
• Works with multigene
• Data validation algorithm implemented

See tutorial for detailed usage

Requirements

• Conda environment (See https://www.anaconda.com/products/individual to how to install conda environment)

Windows

1. Install visual c++ here
2. conda create -n FunVIP python>=3.8
3. conda activate FunVIP
4. pip install FunVIP
5. run FunVIP --test Terrei --email [your email] to check installation

• For upgrade use this command pip install FunVIP --upgrade

Linux

1. conda create -n FunVIP python>=3.8
2. conda activate FunVIP
3. pip install FunVIP
4. conda install -c bioconda raxml iqtree modeltest-ng mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree
5. run FunVIP --test Terrei --email [your email] to check installation

• For intel mac system, this method probably work, but we couldn't test it because we don't have any intel mac device. We're looking for feedbacks in intel mac

Apple Silicon Mac

1. CONDA_SUBDIR=osx-64 conda create -n FunVIP python>=3.8
2. conda activate FunVIP
3. conda config --env --set subdir osx-64
4. conda install pyqt
5. pip install FunVIP
6. conda install -c bioconda raxml iqtree mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree
7. run FunVIP --test Terrei --email [your email] to check installation

Installation from source (For developers and core users)

• this is for developmental steps

1. git clone https://github.com/Changwanseo/FunVIP.git
2. Move to ~/FunVIP
3. conda create -n FunVIP python=3.10
4. conda activate FunVIP
5. pip install ./
6. run FunVIP --test Terrei --email [your email] to check installation

Usage

FunVIP --db {Your database file} --query {Your query file} --email {Your email} --gene {Your genes} --preset {fast or accurate}

Example

FunVIP --db Penicillium.xlsx --query Query.xlsx --email {Your email} --gene ITS BenA RPB2 CaM --preset fast

* See documentation for detailed usage

How to make database?

See example database here

Results

• Section Assignment.xlsx : Your clustering result is here. You can find which of your sequences are clustered to which section
• Identification_result.xlsx : Your final identification result. Shows how your sequences were assigned to species level through tree-based identification
• report.xlsx : overall statistics about the tree. If your find taxon ends with numbers, these taxon are found to be paraphyletic, so should be checked
• /Tree/{section}_{gene}.svg : Final collapsed tree in svg format. Can be edited in vector graphics programs, or in powerpoint (by ungroup)
• /Tree/{section}_{gene}_original.svg : Uncollapsed tree for inspection

How does FunVIP work?

License

GPL 3.0

funid's Issues

Logging with ANSI colors not working with certain prompt

We should edit this with this code

try:
    from colorama import init
    init()  # Initialize colorama on Windows
    SUPPORTS_COLOR = sys.stdout.isatty()
except ImportError:
    SUPPORTS_COLOR = False

Log "Total XXX sequences parsed from query" shows unusual sequencew number.

The log seems to show query+db numbers
However, it would be better to show both query numbers and db numbers in more detailed way

Bugs fix & Improvements required

1. Bug fixes
   1.1 Weird Exception happens during outgroup selection (should find the case)
   1.2 When error occurs during input management, the information goes directly to result without modifications (should find the case)
   1.3 When no corresponding sequence exists in query, the result should be "no sequence" rather than "error"

2. Code improvements
   2.1 Better version control of implied softwares
   2.2 Seperate is_valid_accession and is_valid_sequence function from manage_input.py
   2.3 Make it quiet during unidecode, makeblastdb, modeltest and mafft
   2.4 add overall input command to report

3. Installation issues
   3.1 Change FunID to FunIP in pypi and conda
   3.2 Find installation fails in diverse environment

4. Long term development
   4.1 Move multiprocessing to Ray
   4.2 Multiprocessing logging

Make tutorial