Caltha

A python package for processing UMI tagged mixed amplicon metabarcoding data.

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 (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.

Package links

PyPI

Source(s)

Python Software Foundation,
Python 3.8+. 2019.
Python
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
Augspurger T, Ayd W, Bartak C, Battiston P, Cloud P, Garcia M,
Python Data Analysis Library.
Pandas
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The uncompromising Python code formatter.
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Ziadé T, Cordasco I,
Your tool for style guide enforcement.
Flake8
Sottile A, Struys K, Kuehl C, Finkle M,
A framework for managing and maintaining multi-language pre-commit hooks.
Pre-commit
Python Software Foundation,
The Python Package index.
PyPI
Du L,
A lightweight Python C extension for easy access to sequences from plain and gzipped fasta/q files.
Pyfastx
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

Author(s)

Jasper Boom

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/>.