dinopy 3.0.0

DNA input and output library for Python and Cython. Includes reader and writer for FASTA and FASTQ files, support for samtools faidx files, and generators for solid and gapped q-grams (k-mers).

Dinopy - DNA input and output for Python and Cython

Dinopy’s goal is to make files containing biological sequences easily and efficiently accessible for Python and Cython programmers, allowing them to focus on their application instead of file-io.

#!python

import dinopy
fq_reader = dinopy.FastqReader("reads.fastq")
for sequence, name, quality in fq_reader.reads(quality_values=True):
    if some_function(quality):
        analyze(seq)

Features

• Easy to use reader and writer for FASTA-, FASTQ-, and SAM-files.

• Specifiable data type and representation for return values (bytes, bytearrays, strings and integers see dtype for more information).

• Implemented in Cython for additional speedup.

• Offers a Cython API to avoid introducing Python code into Cython projects.

• Works directly on gzipped files.

• Iterators for q-grams of a sequence (also allowing shaped q-grams).

• (Reverse) complement.

• Chromosome selection from FASTA files.

Getting Started

• If you are new to dinopy you can get started by following the first-steps tutorial.

• A full list of features, as well as the documentation, can be found here.

Installation

Dinopy can be installed with pip:

$ pip install dinopy

or with conda:

$ conda install -c bioconda dinopy

Additionally, dinopy can be downloaded from Bitbucket and compiled using its setup.py:

1. Download source code from bitbucket.

2. Install globally:

   $ python setup.py install

   or only for the current user:

   $ python setup.py install --user

3. Use dinopy:

   $ python
   
   >>> import dinopy

Installation requirements

• python >= 3.8

• numpy >= 1.17

• cython >= 3.0.0

• C and C++ compilers, for example from build-essentials (Linux) or Xcode (OSX)

We recommend using anaconda and the bioconda channel.

$ conda config --add channels bioconda
$ conda create -n dinoenv dinopy

Platform support

Dinopy has been tested on Ubuntu, Arch Linux and OS X (Yosemite and El Capitan).

We do not officially support Windows - dinopy will probably work, but there might be problems due to different linebreak styles; we assume \n as separator but the probability to encounter files with \r\n as line-separator might be higher on Windows.

Contact

If you want to report a bug or want to suggest a new feature, feel free to do so over at bitbucket.

Email:

• Henning Timm: name.surname <at> tu-dortmund.de

• Till Hartmann: name.surname <at> tu-dortmund.de

License

Dinopy is Open Source and licensed under the MIT License.