htsworkflow/pipelines/test/test_genomemap.py

   1 #!/usr/bin/env python
   2 """More direct synthetic test cases for the eland output file processing
   3 """
   4 import os
   5 from StringIO import StringIO
   6 import shutil
   7 import tempfile
   8 import unittest
   9
  10 from htsworkflow.pipelines.runfolder import ElementTree
  11 from htsworkflow.pipelines import genomemap
  12
  13 class TestGenomeMap(unittest.TestCase):
  14     def test_genomesizes_xml(self):
  15         xml = ElementTree.fromstring("""<sequenceSizes>
  16         <chromosome fileName="chr2.fa" contigName="chr2" totalBases="181748087"/>
  17         <chromosome fileName="chr1.fa" contigName="chr1" totalBases="197195432"/>
  18  </sequenceSizes>
  19 """)
  20         g = genomemap.GenomeMap()
  21         g.build_map_from_element(xml)
  22
  23         self.assertTrue('chr1.fa' in g)
  24         self.assertEqual(g['chr1.fa'], 'mm9/chr1.fa')
  25
  26     def test_simulated_genome_dir(self):
  27         vlds = [genomemap.vldInfo('chr1.fa.vld', False),
  28                 genomemap.vldInfo('chr2.fa.vld', False),
  29                 genomemap.vldInfo('chr3.fa.vld', False),
  30                 genomemap.vldInfo('Lambda.fa.vld', True),]
  31
  32         g = genomemap.GenomeMap()
  33         g.build_map_from_dir('mm9', vlds)
  34
  35         self.assertTrue('chr1.fa' in g)
  36         self.assertEqual(len(g), 4)
  37         self.assertEqual(g['chr1.fa'], 'mm9/chr1.fa')
  38         self.assertEqual(g['Lambda.fa'], 'Lambda.fa')
  39
  40     def test_genome_dir(self):
  41         g = genomemap.GenomeMap()
  42         names = ['chr1', 'chr2', 'chr3']
  43         tempdir = None
  44         try:
  45             tempdir = tempfile.mkdtemp(prefix='tmp_mm9')
  46             for base in names:
  47                 name = os.path.join(tempdir, base + '.fa.vld')
  48                 stream = open(name, 'w')
  49                 stream.write(name)
  50                 stream.close()
  51             g.scan_genome_dir(tempdir)
  52         finally:
  53             if tempdir is not None:
  54                 shutil.rmtree(tempdir)
  55
  56         temppath, tempgenome = os.path.split(tempdir)
  57         self.assertTrue('chr1.fa' in g)
  58         self.assertEqual(len(g), 3)
  59         self.assertEqual(g['chr1.fa'], '{0}/chr1.fa'.format(tempgenome))
  60 if __name__ == "__main__":
  61     unittest.main()