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توضیحات

A python package to process UMI tagged mixed amplicon metabarcoding data.

ویژگی	مقدار
سیستم عامل	-
نام فایل	caltha-0.6
نام	caltha
نسخه کتابخانه	0.6
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Jasper Boom
ایمیل نویسنده	jboom@infernum.nl
آدرس صفحه اصلی	https://github.com/JasperBoom/caltha
آدرس اینترنتی	https://pypi.org/project/caltha/
مجوز	-

# 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/>. ```

نیازمندی

مقدار	نام
>=1.0.5	pandas
>=1.19.0	numpy
>=0.6.13	pyfastx
>=1.77	biopython

زبان مورد نیاز

مقدار	نام
>=3.8	Python

نحوه نصب

نصب پکیج whl caltha-0.6:

pip install caltha-0.6.whl

نصب پکیج tar.gz caltha-0.6:

pip install caltha-0.6.tar.gz