Python
SeQuiLa’s Python API
Table of Contents
Watchout
Check Configuration page for other configuration options that applicable for all types of APIs.sequila
Entrypoint to Sequila - tool for large-scale genomics on Spark.
SequilaSession Objects
class SequilaSession(SparkSession)
Wrapper for SparkSession.
Builder Objects
class Builder(SparkSession.Builder)
Builder for :class:SequilaSession.
getOrCreate
def getOrCreate()
Get an existing :class:SequilaSession.
This is to add SequilaSession wrapper around SparkSession.
Examples
from pysequila import SequilaSession
ss = SequilaSession \
.builder \
.getOrCreate()
coverage
def coverage(path: str, refPath: str) -> DataFrame
Create a :class:DataFrame with depth of coverage for a specific aligment file.
.. versionadded:: 0.3.0
Parameters
| Parameter Name | Type | Meaning |
|---|---|---|
| path | str | the alignment file in BAM/CRAM format (with an index file) |
| refPath | str | the reference file in FASTA format (with an index file) |
Returns
:class:DataFrame
Examples
>>> ss.coverage(bam_file, ref_file).show(1)
+------+---------+-------+---+--------+
|contig|pos_start|pos_end|ref|coverage|
+------+---------+-------+---+--------+
| 1| 34| 34| R| 1|
+------+---------+-------+---+--------+
only showing top 1 row
pileup
def pileup(path: str, refPath: str, qual: bool) -> DataFrame
Create a :class:DataFrame with pileup for a specific aligment file.
.. versionadded:: 0.3.0
Parameters
| Parameter Name | Type | Meaning |
|---|---|---|
| path | str | the alignment file in BAM/CRAM format (with an index file) |
| refPath | str | the reference file in FASTA format (with an index file) |
| qual | bool(True) | whether to include base qualities pileup in the output |
Returns
:class:DataFrame
Examples
>>> ss.pileup(bam_file, ref_file, True).where("alts IS NOT NULL").show(1)
+------+---------+-------+---+--------+--------+-----------+---------+--------------------+
|contig|pos_start|pos_end|ref|coverage|countRef|countNonRef| alts| quals|
+------+---------+-------+---+--------+--------+-----------+---------+--------------------+
| 1| 69| 69| A| 7| 6| 1|{99 -> 1}|{65 -> [0, 0, 0, ...|
+------+---------+-------+---+--------+--------+-----------+---------+--------------------+
only showing top 1 row
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Last modified February 1, 2023: fix:race condition for local[n] in toCoverage method (#172) (a49c32b)