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)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| dna_parser-0.6.0.tar.gz | 51.3 kB | Without provenance | Details for dna_parser-0.6.0.tar.gz |
Built distributions (wheels)
Total release size: 46.6 MB
Release files / dna_parser-0.6.0.tar.gz
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Release files / dna_parser-0.6.0-cp313-cp313-manylinux_2_17_i686.manylinux2014_i686.whl
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| Size | 869.3 kB |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | dna_parser-0.6.0-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
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| Size | 685.8 kB |
| Tags | CPython 3.13 Linux glibc 2.17+ ARMv7l |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | dna_parser-0.6.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 724.5 kB |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp313-cp313-macosx_11_0_arm64.whl
| Download URL | dna_parser-0.6.0-cp313-cp313-macosx_11_0_arm64.whl |
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| Size | 718.3 kB |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp313-cp313-macosx_10_12_x86_64.whl
| Download URL | dna_parser-0.6.0-cp313-cp313-macosx_10_12_x86_64.whl |
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| Size | 774.1 kB |
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Release files / dna_parser-0.6.0-cp312-cp312-win_amd64.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-win_amd64.whl |
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| Size | 691.2 kB |
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Release files / dna_parser-0.6.0-cp312-cp312-win32.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-win32.whl |
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| Size | 616.9 kB |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-musllinux_1_2_x86_64.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-musllinux_1_2_x86_64.whl |
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| Size | 1.0 MB |
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Release files / dna_parser-0.6.0-cp312-cp312-musllinux_1_2_i686.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-musllinux_1_2_i686.whl |
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| Size | 1.1 MB |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-musllinux_1_2_armv7l.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-musllinux_1_2_armv7l.whl |
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| Size | 977.2 kB |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-musllinux_1_2_aarch64.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-musllinux_1_2_aarch64.whl |
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| Size | 929.8 kB |
| Tags | CPython 3.12 Linux musl 1.2+ ARM64 |
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Release files / dna_parser-0.6.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 814.7 kB |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl |
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| Size | 807.3 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ IBM System/390x |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
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| Size | 945.3 kB |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl |
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| Size | 870.0 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-32 |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
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| Size | 686.8 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ ARMv7l |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 723.4 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ ARM64 |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-macosx_11_0_arm64.whl |
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| Size | 718.5 kB |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp312-cp312-macosx_10_12_x86_64.whl
| Download URL | dna_parser-0.6.0-cp312-cp312-macosx_10_12_x86_64.whl |
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| Size | 774.1 kB |
| Tags | CPython 3.12 macOS 10.12+ x86-64 |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-win_amd64.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-win_amd64.whl |
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| Size | 695.0 kB |
| Tags | CPython 3.11 Windows x86-64 |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-win32.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-win32.whl |
|---|---|
| Size | 623.4 kB |
| Tags | CPython 3.11 Windows x86-32 |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-musllinux_1_2_x86_64.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-musllinux_1_2_x86_64.whl |
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| Size | 1.0 MB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-64 |
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No |
| Uploaded via |
maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-musllinux_1_2_i686.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-musllinux_1_2_i686.whl |
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| Size | 1.1 MB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-32 |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-musllinux_1_2_armv7l.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-musllinux_1_2_armv7l.whl |
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| Size | 978.1 kB |
| Tags | CPython 3.11 Linux musl 1.2+ ARMv7l |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-musllinux_1_2_aarch64.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-musllinux_1_2_aarch64.whl |
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| Size | 931.8 kB |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 820.0 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
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No |
| Uploaded via |
maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl |
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| Size | 809.1 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ IBM System/390x |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
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| Size | 951.6 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ PowerPC 64-le |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl |
|---|---|
| Size | 874.9 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-32 |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 688.0 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ ARMv7l |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 724.9 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ ARM64 |
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SHA-256 checksum How to use checksums |
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No |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-macosx_11_0_arm64.whl |
|---|---|
| Size | 722.8 kB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
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maturin/1.15.0
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Release files / dna_parser-0.6.0-cp311-cp311-macosx_10_12_x86_64.whl
| Download URL | dna_parser-0.6.0-cp311-cp311-macosx_10_12_x86_64.whl |
|---|---|
| Size | 769.8 kB |
| Tags | CPython 3.11 macOS 10.12+ x86-64 |
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SHA-256 checksum How to use checksums |
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maturin/1.15.0
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Security for dna-parser 0.6.0
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