def test_realignbam():
'It test the GATK realigner'
sam_test_dir = os.path.join(TEST_DATA_DIR, 'samtools')
bam_path = os.path.join(sam_test_dir, 'seqs.bam')
reference_path = os.path.join(sam_test_dir, 'reference.fasta')
out_bam = NamedTemporaryFile(suffix='.bam')
realign_bam(bam_path, reference_path, out_bam.name, threads=THREADS)
out_bam.close()
def run(self):
'''It runs the analysis.'''
self._log({'analysis_started':True})
settings = self._project_settings
project_path = settings['General_settings']['project_path']
tmp_dir = settings['General_settings']['tmpdir']
inputs = self._get_input_fpaths()
bam_path = inputs['bam']
bam_fpath = bam_path.last_version
reference_path = inputs['reference']
#memory for the java programs
osettings = settings['Other_settings']
java_mem = osettings['java_memory']
picard_path = osettings['picard_path']
gatk_path = osettings['gatk_path']
#we need a temporary path
temp_bam = NamedTemporaryFile(suffix='.bam')
temp_bam_fpath = temp_bam.name
temp_bam.close()
#do the realigment
realign_bam(bam_fpath=bam_fpath,
reference_fpath=reference_path.last_version,
out_bam_fpath=temp_bam_fpath,
java_conf={'java_memory':java_mem,
'picard_path':picard_path,
'gatk_path':gatk_path},
threads=self.threads,
tmp_dir=tmp_dir)
#a new version for the original bam
out_bam_fpath = bam_path.next_version
shutil.move(temp_bam_fpath, out_bam_fpath)
self._log({'analysis_finished':True})