{ "info": { "author": "Jasper Boom", "author_email": "jboom@infernum.nl", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "License :: OSI Approved :: GNU Affero General Public License v3", "Natural Language :: English", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3.8", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# Caltha\nA python package for processing UMI tagged mixed amplicon metabarcoding data.\n\n[![Code Style: Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n\n## Installation\nThe current version of __Caltha__ requires Python 3.8+.\n\nTo install __Caltha__, simply run the pip install command:\n```\npip install caltha\n```\n\nNOTE: __Caltha__ does require one more dependency which can not be installed\nwith the __Caltha__ pip or conda package. This dependency is\n[vsearch](https://github.com/torognes/vsearch) (2.14.2). \nExecuting the following conda install command should install the dependency.\n```\nconda install -c bioconda vsearch\n```\n\n## How to run\n__Caltha__ can be run directly from the command line.\n```\nusage: caltha [-h] [-v] [-i FLINPUT] [-t FLTABULAR] [-z FLPREZIP] [-b FLBLAST]\n [-f STRFORMAT] [-l STRLOCATION] [-a STRANCHOR] [-u INTUMILENGTH]\n [-y FLTIDENTITY] [-c INTABUNDANCE] [-w STRFORWARD]\n [-r STRREVERSE] [-d STRDIRECTORY] [-@ INTTHREADS]\n\nA python package for processing UMI tagged mixed amplicon metabarcoding data.\n\noptional arguments:\n -h, --help show this help message and exit\n -v, --version show program's version number and exit\n -i FLINPUT, --input FLINPUT\n The input fasta/fastq file(s). This can either be a\n zip archive or a single fasta/fastq file.\n -t FLTABULAR, --tabular FLTABULAR\n The output tabular zip file.\n -z FLPREZIP, --zip FLPREZIP\n The pre validation zip file.\n -b FLBLAST, --blast FLBLAST\n The output blast zip file.\n -f STRFORMAT, --format STRFORMAT\n The format of the input file\n [fasta/fastq]. (default: fasta)\n -l STRLOCATION, --location STRLOCATION\n Search for UMIs at the 5'-end [umi5], 3'-end [umi3] or \n at the 5'-end and 3'-end [umidouble]. (default: umi5)\n -a STRANCHOR, --anchor STRANCHOR\n Which anchor type to use\n [primer/adapter/zero]. (default: primer)\n -u INTUMILENGTH, --length INTUMILENGTH\n The length of the UMI sequence. (default: 5)\n -y FLTIDENTITY, --identity FLTIDENTITY\n The identity percentage with which to perform the\n validation. (default: 0.97)\n -c INTABUNDANCE, --abundance INTABUNDANCE\n The minimum abundance of a sequence in order for it\n to be included during validation. (default: 1)\n -w STRFORWARD, --forward STRFORWARD\n The 5'-end anchor nucleotides.\n -r STRREVERSE, --reverse STRREVERSE\n The 3'-end anchor nucleotides.\n -d STRDIRECTORY, --directory STRDIRECTORY\n The location of the temporary working directory\n (not created by program). (default: .)\n -@ INTTHREADS, --threads INTTHREADS\n The number of threads to run Caltha\n with. (default: number of threads available on system)\n\nThis python package requires one extra dependency which can be easily\ninstalled with conda (conda install -c bioconda vsearch=2.14.2).\n```\n\nFurther documentation can be found [here](https://jasperboom.github.io/caltha/).\n\n## Package links\n* [PyPI](https://pypi.org/project/caltha/)\n\n## Source(s)\n* __Python Software Foundation__, \n Python 3.8+. 2019. \n [Python](https://www.python.org/)\n* __Rognes T, Flouri T, Nichols B, Quince C, Mahe F__, \n VSEARCH: A versatile open source tool for metagenomics. \n PeerJ. 2016. __doi: 10.7717/peerj.2584__ \n [vsearch](https://github.com/torognes/vsearch)\n* __Augspurger T, Ayd W, Bartak C, Battiston P, Cloud P, Garcia M__, \n Python Data Analysis Library. \n [Pandas](https://pandas.pydata.org/)\n* __Langa L, Willing C, Meyer C, Zijlstra J, Naylor M, Dollenstein Z__, \n The uncompromising Python code formatter. \n [Black](https://black.readthedocs.io/en/stable/)\n* __Ziad\u00e9 T, Cordasco I__, \n Your tool for style guide enforcement. \n [Flake8](http://flake8.pycqa.org/en/latest/index.html)\n* __Sottile A, Struys K, Kuehl C, Finkle M__, \n A framework for managing and maintaining multi-language pre-commit hooks. \n [Pre-commit](https://pre-commit.com/)\n* __Python Software Foundation__, \n The Python Package index. \n [PyPI](https://pypi.org/)\n* __Du L__, \n A lightweight Python C extension for easy access to sequences from plain and\n gzipped fasta/q files. \n [Pyfastx](https://pyfastx.readthedocs.io/en/latest/)\n* __Cock P, Antao T, Chang J, Chapman B, Cox C, Dalke A__, \n Biopython: freely available Python tools for computational molecular biology\n and bioinformatics. \n Bioinformatics. 2009; 25(11): 1422-1423. __doi: 10.1093/bioinformatics/btp163__ \n [Biopython](https://biopython.org/)\n\n## Author(s)\n* [Jasper Boom](https://github.com/JasperBoom)\n\n## Citation\n* __Boom J__, Caltha. \n GitHub repository: https://github.com/JasperBoom/caltha\n\n```\nCopyright (C) 2018 Jasper Boom\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU Affero General Public License version 3 as\npublished by the Free Software Foundation.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\nGNU Affero General Public License for more details.\n\nYou should have received a copy of the GNU Affero General Public License\nalong with this program. If not, see .\n```\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/JasperBoom/caltha", "keywords": "UMI Metabarcoding Amplicon", "license": "", "maintainer": "", "maintainer_email": "", "name": "caltha", "package_url": "https://pypi.org/project/caltha/", "platform": "", "project_url": "https://pypi.org/project/caltha/", "project_urls": { "Documentation": "https://jasperboom.github.io/caltha/", "Homepage": "https://github.com/JasperBoom/caltha", "Source": "https://github.com/JasperBoom/caltha/tree/master/src", "Tracker": "https://github.com/JasperBoom/caltha/issues" }, "release_url": "https://pypi.org/project/caltha/0.6/", "requires_dist": [ "pandas (>=1.0.5)", "numpy (>=1.19.0)", "pyfastx (>=0.6.13)", "biopython (>=1.77)" ], "requires_python": ">=3.8", "summary": "A python package to process UMI tagged mixed amplicon metabarcoding data.", 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