def test_shogun_utree(self):
# inserting new prep template
prep_info_dict = {
'SKB8.640193': {'run_prefix': 'S22205_S104'},
'SKD8.640184': {'run_prefix': 'S22282_S102'}}
data = {'prep_info': dumps(prep_info_dict),
# magic #1 = testing study
'study': 1,
'data_type': 'Metagenomic'}
pid = self.qclient.post('/apitest/prep_template/', data=data)['prep']
# inserting artifacts
fp1_1, fp1_2, fp2_1, fp2_2 = self._helper_shogun_bowtie()
data = {
'filepaths': dumps([
(fp1_1, 'raw_forward_seqs'),
(fp1_2, 'raw_reverse_seqs'),
(fp2_1, 'raw_forward_seqs'),
(fp2_2, 'raw_reverse_seqs')]),
'type': "per_sample_FASTQ",
'name': "Test Shogun artifact",
'prep': pid}
aid = self.qclient.post('/apitest/artifact/', data=data)['artifact']
self.params['input'] = aid
self.params['Aligner tool'] = 'utree'
data = {'user': '******',
'command': dumps(['qp-shogun', '012020', 'Shogun v1.0.7']),
'status': 'running',
'parameters': dumps(self.params)}
jid = self.qclient.post('/apitest/processing_job/', data=data)['job']
out_dir = mkdtemp()
self._clean_up_files.append(out_dir)
success, ainfo, msg = shogun(self.qclient, jid, self.params, out_dir)
self.assertEqual("", msg)
self.assertTrue(success)
# we are expecting 1 artifacts in total
pout_dir = partial(join, out_dir)
self.assertCountEqual(ainfo, [
ArtifactInfo('Shogun Alignment Profile', 'BIOM',
[(pout_dir('otu_table.alignment.profile.biom'),
'biom'),
(pout_dir('alignment.utree.tsv.xz'), 'log')]),
ArtifactInfo('Taxonomic Predictions - phylum', 'BIOM',
[(pout_dir('otu_table.redist.phylum.biom'),
'biom')]),
ArtifactInfo('Taxonomic Predictions - genus', 'BIOM',
[(pout_dir('otu_table.redist.genus.biom'),
'biom')]),
ArtifactInfo('Taxonomic Predictions - species', 'BIOM',
[(pout_dir('otu_table.redist.species.biom'),
'biom')])])
def test_shogun_utree(self):
# generating filepaths
in_dir = mkdtemp()
self._clean_up_files.append(in_dir)
fp1_1 = join(in_dir, 'S22205_S104_L001_R1_001.fastq.gz')
fp1_2 = join(in_dir, 'S22205_S104_L001_R2_001.fastq.gz')
fp2_1 = join(in_dir, 'S22282_S102_L001_R1_001.fastq.gz')
fp2_2 = join(in_dir, 'S22282_S102_L001_R2_001.fastq.gz')
copyfile('support_files/S22205_S104_L001_R1_001.fastq.gz', fp1_1)
copyfile('support_files/S22205_S104_L001_R2_001.fastq.gz', fp1_2)
copyfile('support_files/S22282_S102_L001_R1_001.fastq.gz', fp2_1)
copyfile('support_files/S22282_S102_L001_R2_001.fastq.gz', fp2_2)
# inserting new prep template
prep_info_dict = {
'SKB8.640193': {
'run_prefix': 'S22205_S104'
},
'SKD8.640184': {
'run_prefix': 'S22282_S102'
}
}
data = {
'prep_info': dumps(prep_info_dict),
# magic #1 = testing study
'study': 1,
'data_type': 'Metagenomic'
}
pid = self.qclient.post('/apitest/prep_template/', data=data)['prep']
# inserting artifacts
data = {
'filepaths':
dumps([(fp1_1, 'raw_forward_seqs'), (fp1_2, 'raw_reverse_seqs'),
(fp2_1, 'raw_forward_seqs'), (fp2_2, 'raw_reverse_seqs')]),
'type':
"per_sample_FASTQ",
'name':
"Test Shogun artifact",
'prep':
pid
}
aid = self.qclient.post('/apitest/artifact/', data=data)['artifact']
self.params['input'] = aid
self.params['Aligner tool'] = 'utree'
data = {
'user': '******',
'command': dumps(['qp-shogun', '0.0.1', 'Shogun']),
'status': 'running',
'parameters': dumps(self.params)
}
jid = self.qclient.post('/apitest/processing_job/', data=data)['job']
out_dir = mkdtemp()
self._clean_up_files.append(out_dir)
success, ainfo, msg = shogun(self.qclient, jid, self.params, out_dir)
self.assertEqual("", msg)
self.assertTrue(success)
# we are expecting 2 artifacts in total
self.assertEqual(2, len(ainfo))
obs_func_fps = []
obs_redist_fps = []
ainfo_func = ainfo[0]
ainfo_redist = ainfo[1]
self.assertEqual('BIOM', ainfo_func.artifact_type)
self.assertEqual('BIOM', ainfo_redist.artifact_type)
obs_func_fps = ainfo_func.files
obs_redist_fps = ainfo_redist.files
od = partial(join, out_dir)
func_prefix = "species"
exp_func_fps = [
od("otu_table.%s.kegg.modules.coverage.biom" % func_prefix),
od("otu_table.%s.kegg.modules.biom" % func_prefix),
od("otu_table.%s.kegg.pathways.coverage.biom" % func_prefix),
od("otu_table.%s.kegg.pathways.biom" % func_prefix),
od("otu_table.%s.kegg.biom" % func_prefix),
od("otu_table.%s.normalized.biom" % func_prefix)
]
exp_redist_fps = [
od('otu_table.genus.redist.biom'),
od('otu_table.species.redist.biom'),
od('otu_table.strain.redist.biom')
]
self.assertEqual(obs_func_fps, exp_func_fps)
self.assertEqual(obs_redist_fps, exp_redist_fps)
def test_shogun_utree(self):
# generating filepaths
in_dir = mkdtemp()
self._clean_up_files.append(in_dir)
fp1_1 = join(in_dir, 'S22205_S104_L001_R1_001.fastq.gz')
fp1_2 = join(in_dir, 'S22205_S104_L001_R2_001.fastq.gz')
fp2_1 = join(in_dir, 'S22282_S102_L001_R1_001.fastq.gz')
fp2_2 = join(in_dir, 'S22282_S102_L001_R2_001.fastq.gz')
copyfile('support_files/S22205_S104_L001_R1_001.fastq.gz', fp1_1)
copyfile('support_files/S22205_S104_L001_R2_001.fastq.gz', fp1_2)
copyfile('support_files/S22282_S102_L001_R1_001.fastq.gz', fp2_1)
copyfile('support_files/S22282_S102_L001_R2_001.fastq.gz', fp2_2)
# inserting new prep template
prep_info_dict = {
'SKB8.640193': {
'run_prefix': 'S22205_S104'
},
'SKD8.640184': {
'run_prefix': 'S22282_S102'
}
}
data = {
'prep_info': dumps(prep_info_dict),
# magic #1 = testing study
'study': 1,
'data_type': 'Metagenomic'
}
pid = self.qclient.post('/apitest/prep_template/', data=data)['prep']
# inserting artifacts
data = {
'filepaths':
dumps([(fp1_1, 'raw_forward_seqs'), (fp1_2, 'raw_reverse_seqs'),
(fp2_1, 'raw_forward_seqs'), (fp2_2, 'raw_reverse_seqs')]),
'type':
"per_sample_FASTQ",
'name':
"Test Shogun artifact",
'prep':
pid
}
aid = self.qclient.post('/apitest/artifact/', data=data)['artifact']
self.params['input'] = aid
self.params['Aligner tool'] = 'utree'
data = {
'user': '******',
'command': dumps(['qp-shogun', '0.1.4', 'Shogun']),
'status': 'running',
'parameters': dumps(self.params)
}
jid = self.qclient.post('/apitest/processing_job/', data=data)['job']
out_dir = mkdtemp()
self._clean_up_files.append(out_dir)
success, ainfo, msg = shogun(self.qclient, jid, self.params, out_dir)
self.assertEqual("", msg)
self.assertTrue(success)
# we are expecting 1 artifacts in total
self.assertEqual(1, len(ainfo))
ainfo = ainfo[0]
self.assertEqual(ainfo.artifact_type, 'BIOM')
exp = [(join(out_dir, 'otu_table.alignment.profile.biom'), 'biom')]
self.assertCountEqual(ainfo.files, exp)