camembertpy
Cython wrapper for https://github.com/jts/bri with pysam integration.
Installation
From pip repository
pip install camembert-bri
From source
conda approach (recommended)
conda env create -f environment.yml
conda activate camembert
python setup.py install
pip approach
# optional virtualenv:
virtualenv camembert
source camembert/bin/activate
# Installation
pip install -r requirements.txt
python setup.py install
Examples
API
build read index
from camembert import Bri
b = Bri(bam_file)
b.create()
retrieve reads
from camembert import Bri
b = Bri(bam_file)
b.load()
for read in b.get(read_name):
print(read.to_string()) # read is of type pysam.AligmentSegment
CLI
A command line interface is included and mimics the original bri CLI command. For usage, refer to
camembert --help
camembert <subcommand> --help
build read index
camembert index bam_file.bam
retrieve reads
camembert get bam_file.bam read_name
1 maintainer
Release files for camembert-bri 0.0.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| camembert-bri-0.0.2.tar.gz | 58.3 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| camembert_bri-0.0.2-cp38-cp38-manylinux2010_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.12+ x86-64 | Details |
| camembert_bri-0.0.2-cp37-cp37m-manylinux2010_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.12+ x86-64 | Details |
| camembert_bri-0.0.2-cp36-cp36m-manylinux2010_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.12+ x86-64 | Details |
| camembert_bri-0.0.2-cp27-cp27m-manylinux2010_x86_64.whl | CPython 2.7 | CPython 2.7 pymalloc | Linux glibc 2.12+ x86-64 | Details |
Total release size: 34.4 MB
Release files / camembert-bri-0.0.2.tar.gz
| Download URL | camembert-bri-0.0.2.tar.gz |
|---|---|
| Size | 58.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/40.2.0 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.5.6
|
Release files / camembert_bri-0.0.2-cp38-cp38-manylinux2010_x86_64.whl
| Download URL | camembert_bri-0.0.2-cp38-cp38-manylinux2010_x86_64.whl |
|---|---|
| Size | 9.5 MB |
| Tags | CPython 3.8 Linux glibc 2.12+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.2.0 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.8.1
|
Release files / camembert_bri-0.0.2-cp37-cp37m-manylinux2010_x86_64.whl
| Download URL | camembert_bri-0.0.2-cp37-cp37m-manylinux2010_x86_64.whl |
|---|---|
| Size | 8.5 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.12+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.2.0 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.8.1
|
Release files / camembert_bri-0.0.2-cp36-cp36m-manylinux2010_x86_64.whl
| Download URL | camembert_bri-0.0.2-cp36-cp36m-manylinux2010_x86_64.whl |
|---|---|
| Size | 8.5 MB |
| Tags | CPython 3.6 CPython 3.6 pymalloc Linux glibc 2.12+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.2.0 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.8.1
|
Release files / camembert_bri-0.0.2-cp27-cp27m-manylinux2010_x86_64.whl
| Download URL | camembert_bri-0.0.2-cp27-cp27m-manylinux2010_x86_64.whl |
|---|---|
| Size | 7.8 MB |
| Tags | CPython 2.7 CPython 2.7 pymalloc Linux glibc 2.12+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.2.0 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.8.1
|
