pysequila is Python entrypoint to SeQuiLa, an ANSI-SQL compliant solution for efficient sequencing reads processing and genomic intervals querying built on top of Apache Spark. Range joins, depth of coverage and pileup computations are bread and butter for NGS analysis but the high volume of data make them execute very slowly or even failing to compute.
Requirements
Python 3.7
Features
custom data sources for bioinformatics file formats (BAM, CRAM, VCF)
depth of coverage calculations
pileup calculations
reads filtering
efficient range joins
other utility functions
Setup
$ python -m pip install --user pysequila or (venv)$ python -m pip install pysequila
Usage
$ python
>>> from pyspark.sql import SparkSession
>>> spark = SparkSession \
.builder \
.appName(f'{app_name}') \
.getOrCreate()
>>> from sequila import SequilaSession
>>> ss = SequilaSession(spark)
>>> ss.sql ("SELECT * FROM coverage('reads', 'NA12878'")
>>>
ChangeLog
0.1.0 (2020-09-16)
Initial release.
1 maintainer
Release files for pysequila 0.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pysequila-0.1.2.tar.gz | 4.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pysequila-0.1.2-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 8.0 kB
Release files / pysequila-0.1.2.tar.gz
| Download URL | pysequila-0.1.2.tar.gz |
|---|---|
| Size | 4.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/50.3.0 requests-toolbelt/0.9.1 tqdm/4.49.0 CPython/3.7.9
|
Release files / pysequila-0.1.2-py2.py3-none-any.whl
| Download URL | pysequila-0.1.2-py2.py3-none-any.whl |
|---|---|
| Size | 3.1 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/50.3.0 requests-toolbelt/0.9.1 tqdm/4.49.0 CPython/3.7.9
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