Metadata-Version: 2.1
Name: caltha
Version: 0.5
Summary: A python package to process UMI tagged mixed amplicon                 metabarcoding data.
Home-page: https://github.com/JasperBoom/caltha
Author: Jasper Boom
Author-email: jboom@infernum.nl
License: UNKNOWN
Project-URL: Source, https://github.com/JasperBoom/caltha/tree/master/src
Project-URL: Tracker, https://github.com/JasperBoom/caltha/issues
Project-URL: Documentation, https://jasperboom.github.io/caltha/
Description: # Caltha
        A python package to process UMI tagged mixed amplicon metabarcoding data.
        
        ![Anaconda Cloud](https://anaconda.org/jboom/caltha/badges/version.svg)
        ![Last Update](https://anaconda.org/jboom/caltha/badges/latest_release_date.svg)
        ![Downloads](https://anaconda.org/jboom/caltha/badges/downloads.svg)
        [![Code Style: Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
        [![DOI](https://zenodo.org/badge/216898964.svg)](https://zenodo.org/badge/latestdoi/216898964)
        
        ## Installation
        The current version of __Caltha__ requires Python 3.7+.
        
        To install __Caltha__, simply run the pip install command or the conda install command:
        ```
        pip install caltha
        
        conda install -c jboom caltha
        ```
        
        NOTE: __Caltha__ does require one more dependency which can not be installed
        with the __Caltha__ pip or conda package. This dependency is
        [Vsearch](https://github.com/torognes/vsearch) (2.14.1+).  
        Executing the following conda install command should install the dependency.
        ```
        conda install -c bioconda vsearch
        ```
        
        ## How to run
        __Caltha__ can be run directly from the command line.
        ```
        caltha -h
        
        usage: caltha [-h] [-v] [-i FISINPUT] [-t FOSTABULAR] [-z FOSPREZIP]
                      [-b FOSBLAST] [-f DISFORMAT] [-s DISSEARCH] [-a DISAPPROACH]
                      [-u DISUMILENGTH] [-y DISIDENTITY] [-c DISABUNDANCE]
                      [-w DISFORWARD] [-r DISREVERSE] [-d FISDIRECTORY]
                      [-p DISPROCESSES]
        
        A python package to process UMI tagged mixed amplicon metabarcoding data.
        
        optional arguments:
          -h, --help            show this help message and exit
          -v, -version          show program's version number and exit
          -i FISINPUT, -input FISINPUT
                                The location of the input fasta/fastq file(s).
          -t FOSTABULAR, -tabular FOSTABULAR
                                The location of the output tabular zip file.
          -z FOSPREZIP, -zip FOSPREZIP
                                The location of the pre validation zip file.
          -b FOSBLAST, -blast FOSBLAST
                                The location of the output blast zip file.
          -f DISFORMAT, -format DISFORMAT
                                The format of the input file
                                [fasta/fastq/zipfasta/zipfastq].
          -s DISSEARCH, -search DISSEARCH
                                Search UMIs at the 5'-end [umi5], 3'-end [umi3] or at
                                the 5'-end and 3'-end [umidouble]. (default: umi5)
          -a DISAPPROACH, -approach DISAPPROACH
                                The UMI search approach [primer/adapter/zero].
                                (default: primer)
          -u DISUMILENGTH, -length DISUMILENGTH
                                The length of the UMI sequence.
          -y DISIDENTITY, -identity DISIDENTITY
                                The identity percentage with which to perform the
                                validation. (default: 0.97)
          -c DISABUNDANCE, -abundance DISABUNDANCE
                                The minimum abundance of a read in order to be
                                included during validation. (default: 1)
          -w DISFORWARD, -forward DISFORWARD
                                The 5'-end search nucleotides.
          -r DISREVERSE, -reverse DISREVERSE
                                The 3'-end search nucleotides.
          -d FISDIRECTORY, -directory FISDIRECTORY
                                The location where the temporary working directory
                                will be created. (default: .)
          -p DISPROCESSES, -processes DISPROCESSES
                                The number of threads/cores/processes to
                                simultaneously run Caltha with. (default: number of cores available)
        
        This python package requires one extra dependency which can be easily
        installed with conda (conda install -c bioconda vsearch).
        ```
        
        Further documentation can be found [here](https://jasperboom.github.io/caltha/).
        
        ## Package links
        * [PyPI](https://pypi.org/project/caltha/)
        * [Conda](https://anaconda.org/jboom/caltha)
        
        ## Source(s)
        * __Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P__,  
          Galaxy: A platform for interactive large-scale genome analysis.  
          Genome Research. 2005; 15(10) 1451-1455. __doi: 10.1101/gr.4086505__  
          [Galaxy](https://www.galaxyproject.org/)
        * __Python Software Foundation__,  
          Python 3.7+. 2019.  
          [Python](https://www.python.org/)
        * __Rognes T, Flouri T, Nichols B, Quince C, Mahe F__,  
          VSEARCH: A versatile open source tool for metagenomics.  
          PeerJ. 2016. __doi: 10.7717/peerj.2584__  
          [Vsearch](https://github.com/torognes/vsearch)
        * __Augspurger T, Ayd W, Bartak C, Battiston P, Cloud P, Garcia M__,  
          Python Data Analysis Library.  
          [Pandas](https://pandas.pydata.org/)
        * __Langa L, Willing C, Meyer C, Zijlstra J, Naylor M, Dollenstein Z__,  
          The uncompromising Python code formatter.  
          [Black](https://black.readthedocs.io/en/stable/)
        
        ## Author(s)
        * [Jasper Boom](https://github.com/JasperBoom)
        
        ## Citation
        * __Boom J__, Caltha. 
          [![DOI](https://zenodo.org/badge/216898964.svg)](https://zenodo.org/badge/latestdoi/216898964)  
          GitHub repository: https://github.com/JasperBoom/caltha
        
        ```
        Copyright (C) 2018 Jasper Boom (jboom@infernum.nl)
        
        This program is free software: you can redistribute it and/or modify
        it under the terms of the GNU Affero General Public License version 3 as 
        published by the Free Software Foundation.
        
        This program is distributed in the hope that it will be useful,
        but WITHOUT ANY WARRANTY; without even the implied warranty of
        MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
        GNU Affero General Public License for more details.
        
        You should have received a copy of the GNU Affero General Public License
        along with this program. If not, see <https://www.gnu.org/licenses/>.
        ```
        
Keywords: UMI Metabarcoding
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU Affero General Public License v3
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
