Metadata-Version: 2.1
Name: caltha
Version: 0.6
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 for processing UMI tagged mixed amplicon metabarcoding data.
        
        [![Code Style: Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
        
        ## Installation
        The current version of __Caltha__ requires Python 3.8+.
        
        To install __Caltha__, simply run the pip install command:
        ```
        pip install 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) (2.14.2).  
        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.
        ```
        usage: caltha [-h] [-v] [-i FLINPUT] [-t FLTABULAR] [-z FLPREZIP] [-b FLBLAST]
                      [-f STRFORMAT] [-l STRLOCATION] [-a STRANCHOR] [-u INTUMILENGTH]
                      [-y FLTIDENTITY] [-c INTABUNDANCE] [-w STRFORWARD]
                      [-r STRREVERSE] [-d STRDIRECTORY] [-@ INTTHREADS]
        
        A python package for processing 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 FLINPUT, --input FLINPUT
                                The input fasta/fastq file(s). This can either be a
                                zip archive or a single fasta/fastq file.
          -t FLTABULAR, --tabular FLTABULAR
                                The output tabular zip file.
          -z FLPREZIP, --zip FLPREZIP
                                The pre validation zip file.
          -b FLBLAST, --blast FLBLAST
                                The output blast zip file.
          -f STRFORMAT, --format STRFORMAT
                                The format of the input file
                                [fasta/fastq]. (default: fasta)
          -l STRLOCATION, --location STRLOCATION
                                Search for UMIs at the 5'-end [umi5], 3'-end [umi3] or 
                                at the 5'-end and 3'-end [umidouble]. (default: umi5)
          -a STRANCHOR, --anchor STRANCHOR
                                Which anchor type to use
                                [primer/adapter/zero]. (default: primer)
          -u INTUMILENGTH, --length INTUMILENGTH
                                The length of the UMI sequence. (default: 5)
          -y FLTIDENTITY, --identity FLTIDENTITY
                                The identity percentage with which to perform the
                                validation. (default: 0.97)
          -c INTABUNDANCE, --abundance INTABUNDANCE
                                The minimum abundance of a sequence in order for it
                                to be included during validation. (default: 1)
          -w STRFORWARD, --forward STRFORWARD
                                The 5'-end anchor nucleotides.
          -r STRREVERSE, --reverse STRREVERSE
                                The 3'-end anchor nucleotides.
          -d STRDIRECTORY, --directory STRDIRECTORY
                                The location of the temporary working directory
                                (not created by program). (default: .)
          -@ INTTHREADS, --threads INTTHREADS
                                The number of threads to run Caltha
                                with. (default: number of threads available on system)
        
        This python package requires one extra dependency which can be easily
        installed with conda (conda install -c bioconda vsearch=2.14.2).
        ```
        
        Further documentation can be found [here](https://jasperboom.github.io/caltha/).
        
        ## Package links
        * [PyPI](https://pypi.org/project/caltha/)
        
        ## Source(s)
        * __Python Software Foundation__,  
          Python 3.8+. 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/)
        * __Ziadé T, Cordasco I__,  
          Your tool for style guide enforcement.  
          [Flake8](http://flake8.pycqa.org/en/latest/index.html)
        * __Sottile A, Struys K, Kuehl C, Finkle M__,  
          A framework for managing and maintaining multi-language pre-commit hooks.  
          [Pre-commit](https://pre-commit.com/)
        * __Python Software Foundation__,  
          The Python Package index.  
          [PyPI](https://pypi.org/)
        * __Du L__,  
          A lightweight Python C extension for easy access to sequences from plain and
          gzipped fasta/q files.  
          [Pyfastx](https://pyfastx.readthedocs.io/en/latest/)
        * __Cock P, Antao T, Chang J, Chapman B, Cox C, Dalke A__,  
          Biopython: freely available Python tools for computational molecular biology
          and bioinformatics.  
          Bioinformatics. 2009; 25(11): 1422-1423. __doi: 10.1093/bioinformatics/btp163__  
          [Biopython](https://biopython.org/)
        
        ## Author(s)
        * [Jasper Boom](https://github.com/JasperBoom)
        
        ## Citation
        * __Boom J__, Caltha.  
          GitHub repository: https://github.com/JasperBoom/caltha
        
        ```
        Copyright (C) 2018 Jasper Boom
        
        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 Amplicon
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 :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
