Metadata-Version: 2.1
Name: hitac
Version: 1.5.5
Summary: Hierarchical taxonomic classifier
Home-page: https://gitlab.com/dacs-hpi/hitac
Author: Fabio Malcher Miranda
Author-email: fabio.malchermiranda@hpi.de
License: UNKNOWN
Description: # HiTaC
        
        [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![pipeline status](https://gitlab.com/dacs-hpi/hitac/badges/master/pipeline.svg)](https://gitlab.com/dacs-hpi/hitac/-/commits/master) [![coverage report](https://gitlab.com/dacs-hpi/hitac/badges/master/coverage.svg)](https://gitlab.com/dacs-hpi/hitac/-/commits/master)
        
        A hierarchical taxonomic classifier for fungal ITS sequences.
        
        ## Installation
        
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hitac/README.html)
        
        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 be installed using either conda or pip:
        
        ```
        conda install hitac
        pip install hitac
        ```
        
        ## 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
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3
Description-Content-Type: text/markdown
