README.rst

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).