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
Dinopy’s goal is to make files containing biological sequences easily and efficiently accessible for python 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)
- 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).
- Works directly on gzipped files.
- Iterators for q-grams of a sequence (also allowing shaped q-grams).
- (Reverse) complement.
- Chromosome selection from FASTA files.
- Implemented in Cython for additional speedup.
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:
Download source code from bitbucket.
$ python setup.py install
or only for the current user:
$ python setup.py install --user
$ python >>> import dinopy
- python >= 3.3
- numpy >= 1.7
- C and C++ compilers, for example from build-essentials (Linux) or Xcode (OSX)
- Optional: cython >= 0.20
$ conda config --add channels r $ conda config --add channels bioconda $ conda create -n dinoenv dinopy
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.
Features in development
- BAM-writer / reader
- GFF3 parser
- Bisulfite arrays
- quality-trimming for FASTQ parser