Hierarchical taxonomic classifier.
Project description
HiTaC
A hierarchical taxonomic classifier for fungal ITS sequences.
Installation
HiTaC dependends on QIIME 2. We recommend using QIIME 2 version 2020.2. To install QIIME 2 in a new conda environment and activate it, please run:
wget https://data.qiime2.org/distro/core/qiime2-2020.2-py36-linux-conda.yml
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-linux-conda.yml
conda activate qiime2-2020.2
Afterwards, HiTaC can also be installed with conda:
conda install -c bioconda hitac
Alternatively, HiTaC can be installed with pip in an environment where QIIME 2 was previously installed:
pip install hitac
Lastly, HiTaC and all its dependencies can be download as a docker image:
docker pull mirand863/hitac:latest
The downloaded image can then be started with:
docker run -it mirand863/hitac:latest /bin/bash
Input Files
HiTaC accepts taxonomy in TSV format and training and test files in FASTA format. All these files must be previously imported by QIIME 2. For example:
qiime tools import \
--input-path $qfa \
--output-path q-seqs.qza \
--type 'FeatureData[Sequence]'
qiime tools import \
--input-path dbq.fa \
--output-path db-seqs.qza \
--type 'FeatureData[Sequence]'
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-format HeaderlessTSVTaxonomyFormat \
--input-path db-tax.txt \
--output-path db-tax.qza
To train the model and classify, simply run:
qiime hitac classify \
--i-reference-reads db-seqs.qza \
--i-reference-taxonomy db-tax.qza \
--i-query q-seqs.qza \
--o-classification classifier_output.qza --verbose
Running
To see the usage run qiime hitac --help
Usage: qiime hitac [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin wraps HiTaC and supports hierarchical
taxonomic classification.
Plugin website: https://gitlab.com/dacs-hpi/hitac
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
classify HiTaC
Output File
The predictions can be exported from QIIME 2 to a TSV file:
qiime tools export \
--input-path classifier_output.qza \
--output-path output_dir
The first column in the TSV file contains the identifier of the test sequence and the second column holds the predictions made by HiTaC. For example:
Feature ID Taxon Confidence
EU254776;tax=d:Fungi,p:Ascomycota,c:Sordariomycetes,o:Diaporthales,f:Gnomoniaceae,g:Gnomonia; d__Fungi; p__Ascomycota; c__Sordariomycetes; o__Diaporthales; f__Valsaceae; g__Cryptosporella -1
FJ711636;tax=d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Agaricales,f:Marasmiaceae,g:Armillaria; d__Fungi; p__Basidiomycota; c__Agaricomycetes; o__Agaricales; f__Marasmiaceae; g__Armillaria -1
UDB016040;tax=d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Russulales,f:Russulaceae,g:Russula; d__Fungi; p__Basidiomycota; c__Agaricomycetes; o__Russulales; f__Russulaceae; g__Russula -1
GU827310;tax=d:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Ramalinaceae,g:Ramalina; d__Fungi; p__Ascomycota; c__Lecanoromycetes; o__Lecanorales; f__Ramalinaceae; g__Ramalina -1
JN943699;tax=d:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Parmeliaceae,g:Melanohalea; d__Fungi; p__Ascomycota; c__Lecanoromycetes; o__Lecanorales; f__Parmeliaceae; g__Punctelia -1
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