==============
NGS test utils
==============
Utilities for generation of synthetic NGS files.
A simple showcase::
from ngs_test_utils import testcase
class ExampleTestCase(testcase.NgsTestCase):
"""NGS-test-utils showcase."""
def test_example(self):
"""Make a simple GTf and BAM file."""
self.gtf = self.make_gtf([
dict(feature="gene", start=100, end=500, gene_id="G1"),
dict(feature="exon", start=100, end=200, gene_id="G1"),
dict(feature="exon", start=400, end=500, gene_id="G1"),
])
self.bam = self.make_bam(
chroms=[("chr1", 1000)],
segments=[
dict(qname="r1", pos=150, cigar=[(0, 75)]),
dict(qname="r2", pos=250, cigar=[(0, 150)]),
],
)
# Use these files to run your tests...
In the above example you can see:
- Test case class subclasses ``testcase.NgsTestCase`` instead of
``unittest.TestCase``. This class brings in all the methods for
generating synthetic files.
- Methods for generation of files aim to support "Pythonic"
construction of NGS files from scratch. Although the methods try to be
user-friendly, one needs to be familiar with the structure of the
file format.
- Method ``self.make_gtf`` accepts list of GTF segments. Each of these
segments represents a line in a GTF file. Segment is given as a dict
of values that represent columns (and attributes) of a line in GTF
file.
- Method ``self.make_bam`` accepts a list of chromosomes (this is
ingredient for BAM header) and list of segments (for BAM body).
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"description": "==============\nNGS test utils\n==============\n\nUtilities for generation of synthetic NGS files.\n\nA simple showcase::\n\n from ngs_test_utils import testcase\n\n class ExampleTestCase(testcase.NgsTestCase):\n \"\"\"NGS-test-utils showcase.\"\"\"\n\n def test_example(self):\n \"\"\"Make a simple GTf and BAM file.\"\"\"\n\n self.gtf = self.make_gtf([\n dict(feature=\"gene\", start=100, end=500, gene_id=\"G1\"),\n dict(feature=\"exon\", start=100, end=200, gene_id=\"G1\"),\n dict(feature=\"exon\", start=400, end=500, gene_id=\"G1\"),\n ])\n\n self.bam = self.make_bam(\n chroms=[(\"chr1\", 1000)],\n segments=[\n dict(qname=\"r1\", pos=150, cigar=[(0, 75)]),\n dict(qname=\"r2\", pos=250, cigar=[(0, 150)]),\n ],\n )\n\n # Use these files to run your tests...\n\nIn the above example you can see:\n\n- Test case class subclasses ``testcase.NgsTestCase`` instead of\n ``unittest.TestCase``. This class brings in all the methods for\n generating synthetic files.\n- Methods for generation of files aim to support \"Pythonic\"\n construction of NGS files from scratch. Although the methods try to be\n user-friendly, one needs to be familiar with the structure of the\n file format.\n- Method ``self.make_gtf`` accepts list of GTF segments. Each of these\n segments represents a line in a GTF file. Segment is given as a dict\n of values that represent columns (and attributes) of a line in GTF\n file.\n- Method ``self.make_bam`` accepts a list of chromosomes (this is\n ingredient for BAM header) and list of segments (for BAM body).\n",
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