def run(self):
'''It runs the analysis.'''
self._log({'analysis_started':True})
settings = self._project_settings
self._create_output_dirs()['result']
project_name = settings['General_settings']['project_name']
sample_size = settings['Sam_stats']['sampling_size']
project_path = settings['General_settings']['project_path']
inputs = self._get_input_fpaths()
bam_path = inputs['bam']
bam_fpath = bam_path.last_version
bam_fhand = open(bam_fpath)
out_dir = os.path.abspath(self._get_output_dirs()['result'])
summary_fname = os.path.join(out_dir,
BACKBONE_BASENAMES['statistics_file'])
summary_fhand = open(summary_fname, 'w')
# non mapped_reads_fhand
unmapped_fpath = os.path.join(project_path,
BACKBONE_DIRECTORIES['mappings'][0],
BACKBONE_BASENAMES['unmapped_list'])
if os.path.exists(unmapped_fpath):
unmapped_fhand = GzipFile(unmapped_fpath)
else:
unmapped_fhand = None
#The general statistics
bam_general_stats(bam_fhand, summary_fhand, unmapped_fhand)
for kind in ('coverage', 'mapq'):
basename = os.path.join(out_dir, "%s" % (project_name))
bam_fhand.seek(0)
bam_distribs(bam_fhand, kind, basename=basename,
sample_size=sample_size, summary_fhand=summary_fhand,
plot_file_format=PLOT_FILE_FORMAT)
bam_fhand.close()
if unmapped_fhand is not None:
unmapped_fhand.close()
def test_bam_distribs():
'test bam coverage distrib'
sam = NamedTemporaryFile(suffix='.sam')
sam.write(SAM)
sam.flush()
bam_fhand = NamedTemporaryFile()
sam2bam(sam.name, bam_fhand.name)
summary_fhand = StringIO()
distribs = bam_distribs(bam_fhand, 'coverage',
summary_fhand=summary_fhand)
expected = [2547]
assert distribs[('platform', '454')]['distrib'] == expected
assert 'average: 0.13' in summary_fhand.getvalue()
distribs = bam_distribs(bam_fhand, 'mapq')
assert distribs[('platform', '454')]['distrib'][0] == 1
distribs = bam_distribs(bam_fhand, 'mapq', sample_size=100)
assert distribs[('platform', '454')]['distrib'][0] == 1
distribs = bam_distribs(bam_fhand, 'edit_distance')
assert distribs[('platform', '454')]['distrib'][0] == 1
