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dna-parser

dna-parser is a Python library written in Rust to encode (or perform feature extraction on) DNA/RNA sequences for machine learning.

The source code is available on GitHub

The documentation is available here.

Installation

To install dna-parser run:

pip install dna-parser

If there is no Python wheel available for your OS, you can install Rust and re-install dna-parser which should now compile on your machine. Run the following command on Unix-like OS to install Rust:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

or see more options at https://www.rust-lang.org/tools/install.

Quick Start

Loading Sequences

import dna_parser as dps

reader= dps.SequenceReader("path/to/file")
reader.get_sequences()
# Output:
# [agcgcggtgcgc, agcggcgcgtata, ...]

reader.reset() # read all sequences and exhausted the reader so we reset it.
reader.get_ids()
# Output:
#['sequence1', 'sequence2', 'sequence3']

reader.reset()
for seq in reader.get_records():
    print(seq) # seq -> SequenceRecord object
               # with attributes .id .format .seq .qual (if Fastq file)
# Output:
#[ID: sequence1
# Format: Fasta
# Sequence: acgtatgcgtcgtc...
# Quality: None]
#
#[ID: sequence2
# ...

If the file does not fit in memory you can use the batch_size option to return a list containing the desired number of objects.

import dna_parser as dps

reader= dps.SequenceReader("path/to/file.fasta", batch_size=1)
reader.get_sequences()
# Output:
# [agcgcggtgcgc]
reader.get_sequences()
# Output:
# [agcggcgcgtata]

Encoding Sequences

Encoding functions accept any iterables (list, set, tuple etc.) containing strings. It also accepts dna-parser SequenceReader, pysam FastxFile and Biopython SeqIO.read objects.

import dna_parser as dps

sequences= ["agt","acc"]
encodings= dps.onehot_encoding(sequences)
print(encodings)
# Output: list of numpy ndarray
#[[[0 0 1 0]
#  [0 1 0 0]
#  [0 0 0 1]]

# [[0 0 1 0]
#  [1 0 0 0]
#  [1 0 0 0]]]

reader= dps.SequenceReader("path/to/file") #or pysam.FastxFile("path/to/file") or SeqIO.parse("path/to/file", "fasta")
encodings= dps.eiip_encoding(reader)
print(encodings)
# Output: list of numpy ndarray
#[array([0.126 , 0.134 , 0.0806, 0.1335, 0.126 , 0.1335, 0.0806, 0.134]),
# array([0.134 , 0.134 , 0.134 , 0.0806, 0.1335, 0.0806, 0.126 , 0.   ],
# ... ]

Most encodings provide options to pad/trim the sequence and to encode them in parallel for shorter encoding time.

import dna_parser as dps

sequences= ["agt","accgt"]                                
encodings= dps.eiip_encoding(sequences, pad_type="after", pad_length=-2, n_jobs=2) #-2 pad to longest sequence, -1 trim to shortest
print(encodings)                                                                   # 0 no padding, 1+ fixed length trim/padding 
# Output: numpy ndarray
# array([[0.126 , 0.0806, 0.1335, 0.    , 0.    ],
#        [0.126 , 0.134 , 0.134 , 0.0806, 0.1335]])

All encodings with examples are available in the Documentation section.

Metadata

Release files for dna-parser 0.6.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for dna-parser 0.6.0
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dna_parser-0.6.0.tar.gz 51.3 kB Without provenance Details for dna_parser-0.6.0.tar.gz

Built distributions (wheels)

Table of built distributions (wheels) for dna-parser 0.6.0
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dna_parser-0.6.0-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details for dna_parser-0.6.0-cp314-cp314-win_amd64.whl
dna_parser-0.6.0-cp314-cp314-win32.whl CPython 3.14 CPython 3.14 Windows x86-32 Details for dna_parser-0.6.0-cp314-cp314-win32.whl
dna_parser-0.6.0-cp314-cp314-musllinux_1_2_x86_64.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details for dna_parser-0.6.0-cp314-cp314-musllinux_1_2_x86_64.whl
dna_parser-0.6.0-cp314-cp314-musllinux_1_2_i686.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-32 Details for dna_parser-0.6.0-cp314-cp314-musllinux_1_2_i686.whl
dna_parser-0.6.0-cp314-cp314-musllinux_1_2_armv7l.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ ARMv7l Details for dna_parser-0.6.0-cp314-cp314-musllinux_1_2_armv7l.whl
dna_parser-0.6.0-cp314-cp314-musllinux_1_2_aarch64.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details for dna_parser-0.6.0-cp314-cp314-musllinux_1_2_aarch64.whl
dna_parser-0.6.0-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-64 Details for dna_parser-0.6.0-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
dna_parser-0.6.0-cp314-cp314-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ IBM System/390x Details for dna_parser-0.6.0-cp314-cp314-manylinux_2_17_s390x.manylinux2014_s390x.whl
dna_parser-0.6.0-cp314-cp314-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ PowerPC 64-le Details for dna_parser-0.6.0-cp314-cp314-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
dna_parser-0.6.0-cp314-cp314-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-32 Details for dna_parser-0.6.0-cp314-cp314-manylinux_2_17_i686.manylinux2014_i686.whl
dna_parser-0.6.0-cp314-cp314-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARMv7l Details for dna_parser-0.6.0-cp314-cp314-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
dna_parser-0.6.0-cp314-cp314-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARM64 Details for dna_parser-0.6.0-cp314-cp314-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
dna_parser-0.6.0-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details for dna_parser-0.6.0-cp314-cp314-macosx_11_0_arm64.whl
dna_parser-0.6.0-cp314-cp314-macosx_10_12_x86_64.whl CPython 3.14 CPython 3.14 macOS 10.12+ x86-64 Details for dna_parser-0.6.0-cp314-cp314-macosx_10_12_x86_64.whl
dna_parser-0.6.0-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details for dna_parser-0.6.0-cp313-cp313-win_amd64.whl
dna_parser-0.6.0-cp313-cp313-win32.whl CPython 3.13 CPython 3.13 Windows x86-32 Details for dna_parser-0.6.0-cp313-cp313-win32.whl
dna_parser-0.6.0-cp313-cp313-musllinux_1_2_x86_64.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details for dna_parser-0.6.0-cp313-cp313-musllinux_1_2_x86_64.whl
dna_parser-0.6.0-cp313-cp313-musllinux_1_2_i686.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-32 Details for dna_parser-0.6.0-cp313-cp313-musllinux_1_2_i686.whl
dna_parser-0.6.0-cp313-cp313-musllinux_1_2_armv7l.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ ARMv7l Details for dna_parser-0.6.0-cp313-cp313-musllinux_1_2_armv7l.whl
dna_parser-0.6.0-cp313-cp313-musllinux_1_2_aarch64.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details for dna_parser-0.6.0-cp313-cp313-musllinux_1_2_aarch64.whl
dna_parser-0.6.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details for dna_parser-0.6.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
dna_parser-0.6.0-cp313-cp313-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ IBM System/390x Details for dna_parser-0.6.0-cp313-cp313-manylinux_2_17_s390x.manylinux2014_s390x.whl
dna_parser-0.6.0-cp313-cp313-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ PowerPC 64-le Details for dna_parser-0.6.0-cp313-cp313-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
dna_parser-0.6.0-cp313-cp313-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-32 Details for dna_parser-0.6.0-cp313-cp313-manylinux_2_17_i686.manylinux2014_i686.whl
dna_parser-0.6.0-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARMv7l Details for dna_parser-0.6.0-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
dna_parser-0.6.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARM64 Details for dna_parser-0.6.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
dna_parser-0.6.0-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details for dna_parser-0.6.0-cp313-cp313-macosx_11_0_arm64.whl
dna_parser-0.6.0-cp313-cp313-macosx_10_12_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.12+ x86-64 Details for dna_parser-0.6.0-cp313-cp313-macosx_10_12_x86_64.whl
dna_parser-0.6.0-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details for dna_parser-0.6.0-cp312-cp312-win_amd64.whl
dna_parser-0.6.0-cp312-cp312-win32.whl CPython 3.12 CPython 3.12 Windows x86-32 Details for dna_parser-0.6.0-cp312-cp312-win32.whl
dna_parser-0.6.0-cp312-cp312-musllinux_1_2_x86_64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details for dna_parser-0.6.0-cp312-cp312-musllinux_1_2_x86_64.whl
dna_parser-0.6.0-cp312-cp312-musllinux_1_2_i686.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-32 Details for dna_parser-0.6.0-cp312-cp312-musllinux_1_2_i686.whl
dna_parser-0.6.0-cp312-cp312-musllinux_1_2_armv7l.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ ARMv7l Details for dna_parser-0.6.0-cp312-cp312-musllinux_1_2_armv7l.whl
dna_parser-0.6.0-cp312-cp312-musllinux_1_2_aarch64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details for dna_parser-0.6.0-cp312-cp312-musllinux_1_2_aarch64.whl
dna_parser-0.6.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details for dna_parser-0.6.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
dna_parser-0.6.0-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ IBM System/390x Details for dna_parser-0.6.0-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl
dna_parser-0.6.0-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ PowerPC 64-le Details for dna_parser-0.6.0-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
dna_parser-0.6.0-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-32 Details for dna_parser-0.6.0-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl
dna_parser-0.6.0-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARMv7l Details for dna_parser-0.6.0-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
dna_parser-0.6.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details for dna_parser-0.6.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
dna_parser-0.6.0-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details for dna_parser-0.6.0-cp312-cp312-macosx_11_0_arm64.whl
dna_parser-0.6.0-cp312-cp312-macosx_10_12_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.12+ x86-64 Details for dna_parser-0.6.0-cp312-cp312-macosx_10_12_x86_64.whl
dna_parser-0.6.0-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details for dna_parser-0.6.0-cp311-cp311-win_amd64.whl
dna_parser-0.6.0-cp311-cp311-win32.whl CPython 3.11 CPython 3.11 Windows x86-32 Details for dna_parser-0.6.0-cp311-cp311-win32.whl
dna_parser-0.6.0-cp311-cp311-musllinux_1_2_x86_64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details for dna_parser-0.6.0-cp311-cp311-musllinux_1_2_x86_64.whl
dna_parser-0.6.0-cp311-cp311-musllinux_1_2_i686.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-32 Details for dna_parser-0.6.0-cp311-cp311-musllinux_1_2_i686.whl
dna_parser-0.6.0-cp311-cp311-musllinux_1_2_armv7l.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ ARMv7l Details for dna_parser-0.6.0-cp311-cp311-musllinux_1_2_armv7l.whl
dna_parser-0.6.0-cp311-cp311-musllinux_1_2_aarch64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details for dna_parser-0.6.0-cp311-cp311-musllinux_1_2_aarch64.whl
dna_parser-0.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details for dna_parser-0.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
dna_parser-0.6.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ IBM System/390x Details for dna_parser-0.6.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl
dna_parser-0.6.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ PowerPC 64-le Details for dna_parser-0.6.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
dna_parser-0.6.0-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-32 Details for dna_parser-0.6.0-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl
dna_parser-0.6.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARMv7l Details for dna_parser-0.6.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
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