test/test_Parser.py

   1 #!/usr/bin/env python
   2 # Time-stamp: <2024-10-16 00:13:01 Tao Liu>
   3
   4 import unittest
   5
   6 from MACS3.IO.Parser import (guess_parser,
   7                              BEDParser,
   8                              SAMParser,
   9                              BAMParser,
  10                              FragParser)
  11
  12
  13 class Test_auto_guess(unittest.TestCase):
  14
  15     def setUp(self):
  16         self.bedfile = "test/tiny.bed.gz"
  17         self.bedpefile = "test/tiny.bedpe.gz"
  18         self.samfile = "test/tiny.sam.gz"
  19         self.bamfile = "test/tiny.bam"
  20
  21     def test_guess_parser_bed(self):
  22         p = guess_parser(self.bedfile)
  23         self.assertTrue(p.is_gzipped())
  24         self.assertTrue(isinstance(p, BEDParser))
  25
  26     def test_guess_parser_sam(self):
  27         p = guess_parser(self.samfile)
  28         self.assertTrue(p.is_gzipped())
  29         self.assertTrue(isinstance(p, SAMParser))
  30
  31     def test_guess_parser_bam(self):
  32         p = guess_parser(self.bamfile)
  33         self.assertTrue(p.is_gzipped())
  34         self.assertTrue(isinstance(p, BAMParser))
  35
  36
  37 class Test_parsing(unittest.TestCase):
  38     def setUp(self):
  39         self.bedfile = "test/tiny.bed.gz"
  40         self.bedpefile = "test/tiny.bedpe.gz"
  41         self.samfile = "test/tiny.sam.gz"
  42         self.bamfile = "test/tiny.bam"
  43         self.fragfile = "test/test.fragments.tsv.gz"
  44
  45     def test_fragment_file(self):
  46         p = FragParser(self.fragfile)
  47         petrack = p.build_petrack2()
  48         petrack.finalize()
  49         bdg = petrack.pileup_bdg()
  50         bdg2 = petrack.pileup_bdg2()
  51         peaks = bdg.call_peaks(cutoff=10, min_length=200, max_gap=100)
  52         peaks2 = bdg2.call_peaks(cutoff=10, min_length=200, max_gap=100)
  53         print(peaks)
  54         print(peaks2)