'42JUYAAXX/C1-76',
'30221AAXX',
'30221AAXX/C1-33',
+ '30DY0AAXX',
+ '30DY0AAXX/C1-151',
'61MJTAAXX',
'61MJTAAXX/C1-76',
]
'30221AAXX/C1-33/woldlab_090425_HWI-EAS229_0110_30221AAXX_6.srf',
'30221AAXX/C1-33/woldlab_090425_HWI-EAS229_0110_30221AAXX_7.srf',
'30221AAXX/C1-33/woldlab_090425_HWI-EAS229_0110_30221AAXX_8.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_1.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_2.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_3.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_4.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_5.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_6.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_7.srf',
+ '30DY0AAXX/C1-151/woldlab_090725_HWI-EAS229_0110_30DY0AAXX_8.srf',
'61MJTAAXX/C1-76/woldlab_100826_HSI-123_0001_61MJTAAXX_l1_r1.tar.bz2',
'61MJTAAXX/C1-76/woldlab_100826_HSI-123_0001_61MJTAAXX_l2_r1.tar.bz2',
'61MJTAAXX/C1-76/woldlab_100826_HSI-123_0001_61MJTAAXX_l3_r1.tar.bz2',
u'read_length': 76,
u'status': u'Unknown',
u'status_code': None},
+ {u'flowcell': u'30DY0AAXX',
+ u'lane_number': 8,
+ u'paired_end': True,
+ u'read_length': 76,
+ u'status': u'Unknown',
+ u'status_code': None},
{u'flowcell': u'C02F9ACXX',
u'lane_number': 3,
u'paired_end': True,
class TestCondorFastq(unittest.TestCase):
def setUp(self):
+ self.cwd = os.getcwd()
+
self.tempdir = tempfile.mkdtemp(prefix='condorfastq_test')
self.flowcelldir = os.path.join(self.tempdir, 'flowcells')
os.mkdir(self.flowcelldir)
with open(filename, 'w') as stream:
stream.write('testfile')
+ self.subname = unicode('sub-11154')
+ self.subdir = os.path.join(self.tempdir, self.subname)
+ os.mkdir(self.subdir)
+
def tearDown(self):
shutil.rmtree(self.tempdir)
+ os.chdir(self.cwd)
def test_find_archive_sequence(self):
extract = condorfastq.CondorFastqExtract('host',
self.tempdir,
self.logdir)
extract.api = FakeApi()
- result_map = [('11154', '/notarealplace')]
+ result_map = [('11154', self.subname)]
lib_db = extract.find_archive_sequence_files(result_map)
- self.failUnlessEqual(len(lib_db['11154']['lanes']), 4)
+ self.failUnlessEqual(len(lib_db['11154']['lanes']), 5)
lanes = [
lib_db['11154']['lanes'][(u'30221AAXX', 4)],
lib_db['11154']['lanes'][(u'42JUYAAXX', 5)],
lib_db['11154']['lanes'][(u'61MJTAAXX', 6)],
+ lib_db['11154']['lanes'][(u'30DY0AAXX', 8)],
lib_db['11154']['lanes'][(u'C02F9ACXX', 3)],
]
self.failUnlessEqual(len(lanes[0]), 1)
self.failUnlessEqual(len(lanes[1]), 2)
self.failUnlessEqual(len(lanes[2]), 1)
- self.failUnlessEqual(len(lanes[3]), 4)
+ self.failUnlessEqual(len(lanes[3]), 1)
+ self.failUnlessEqual(len(lanes[4]), 4)
def test_find_needed_targets(self):
self.tempdir,
self.logdir)
extract.api = FakeApi()
- result_map = [('11154', '/notarealplace')]
+ result_map = [('11154', self.subname)]
lib_db = extract.find_archive_sequence_files(result_map)
needed_targets = extract.find_missing_targets(result_map,
lib_db)
- self.failUnlessEqual(len(needed_targets), 6)
+ self.failUnlessEqual(len(needed_targets), 7)
srf_30221 = needed_targets[
- u'/notarealplace/11154_30221AAXX_c33_l4.fastq']
+ self.subname + u'/11154_30221AAXX_c33_l4.fastq']
qseq_42JUY_r1 = needed_targets[
- u'/notarealplace/11154_42JUYAAXX_c76_l5_r1.fastq']
+ self.subname + u'/11154_42JUYAAXX_c76_l5_r1.fastq']
qseq_42JUY_r2 = needed_targets[
- u'/notarealplace/11154_42JUYAAXX_c76_l5_r2.fastq']
+ self.subname + u'/11154_42JUYAAXX_c76_l5_r2.fastq']
qseq_61MJT = needed_targets[
- u'/notarealplace/11154_61MJTAAXX_c76_l6.fastq']
+ self.subname + u'/11154_61MJTAAXX_c76_l6.fastq']
split_C02F9_r1 = needed_targets[
- u'/notarealplace/11154_C02F9ACXX_c202_l3_r1.fastq']
+ self.subname + u'/11154_C02F9ACXX_c202_l3_r1.fastq']
split_C02F9_r2 = needed_targets[
- u'/notarealplace/11154_C02F9ACXX_c202_l3_r2.fastq']
+ self.subname + u'/11154_C02F9ACXX_c202_l3_r2.fastq']
self.failUnlessEqual(len(srf_30221['srf']), 1)
self.failUnlessEqual(len(qseq_42JUY_r1['qseq']), 1)
self.tempdir,
self.logdir)
extract.api = FakeApi()
- result_map = [('11154', '/notarealplace')]
+ result_map = [('11154', self.subdir)]
commands = extract.build_condor_arguments(result_map)
srf = commands['srf']
qseq = commands['qseq']
split = commands['split_fastq']
- self.failUnlessEqual(len(srf), 1)
+ self.failUnlessEqual(len(srf), 2)
self.failUnlessEqual(len(qseq), 3)
self.failUnlessEqual(len(split), 2)
- srf_data = {u'/notarealplace/11154_30221AAXX_c33_l4.fastq':
- [u'30221AAXX',
- u'woldlab_090425_HWI-EAS229_0110_30221AAXX_4.srf'],
- }
+ srf_data = {
+ os.path.join(self.subdir, '11154_30221AAXX_c33_l4.fastq'): {
+ 'mid': None,
+ 'ispaired': False,
+ 'sources': [u'woldlab_090425_HWI-EAS229_0110_30221AAXX_4.srf'],
+ 'flowcell': u'30221AAXX',
+ 'target': os.path.join(self.subdir,
+ u'11154_30221AAXX_c33_l4.fastq'),
+ },
+ os.path.join(self.subdir, '11154_30DY0AAXX_c151_l8_r1.fastq'): {
+ 'mid': None,
+ 'ispaired': True,
+ 'flowcell': u'30DY0AAXX',
+ 'sources': [u'woldlab_090725_HWI-EAS229_0110_30DY0AAXX_8.srf'],
+ 'mid': 76,
+ 'target':
+ os.path.join(self.subdir,
+ u'11154_30DY0AAXX_c151_l8_r1.fastq'),
+ 'target_right':
+ os.path.join(self.subdir,
+ u'11154_30DY0AAXX_c151_l8_r2.fastq'),
+ }
+ }
for args in srf:
- args = extract_argument_list(args)
- expected = srf_data[args[3]]
- self.failUnless(expected[0] in args[5])
- self.failUnless(expected[1] in args[0])
-
- qseq_data = {u'/notarealplace/11154_42JUYAAXX_c76_l5_r1.fastq':
- [u'42JUYAAXX',
- u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r1.tar.bz2'],
- u'/notarealplace/11154_61MJTAAXX_c76_l6.fastq':
- ['61MJTAAXX',
- 'woldlab_100826_HSI-123_0001_61MJTAAXX_l6_r1.tar.bz2'],
- u'/notarealplace/11154_42JUYAAXX_c76_l5_r2.fastq':
- ['42JUYAAXX',
- 'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2'],
- }
+ expected = srf_data[args['target']]
+ self.failUnlessEqual(args['ispaired'], expected['ispaired'])
+ self.failUnlessEqual(len(args['sources']), 1)
+ _, source_filename = os.path.split(args['sources'][0])
+ self.failUnlessEqual(source_filename, expected['sources'][0])
+ self.failUnlessEqual(args['target'], expected['target'])
+ if args['ispaired']:
+ self.failUnlessEqual(args['target_right'],
+ expected['target_right'])
+ if 'mid' in expected:
+ self.failUnlessEqual(args['mid'], expected['mid'])
+
+ qseq_data = {
+ os.path.join(self.subdir, '11154_42JUYAAXX_c76_l5_r1.fastq'): {
+ 'istar': True,
+ 'ispaired': True,
+ 'sources': [
+ u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r1.tar.bz2']
+ },
+ os.path.join(self.subdir, '11154_42JUYAAXX_c76_l5_r2.fastq'): {
+ 'istar': True,
+ 'ispaired': True,
+ 'sources': [
+ u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2']
+ },
+ os.path.join(self.subdir, '11154_61MJTAAXX_c76_l6.fastq'): {
+ 'istar': True,
+ 'ispaired': False,
+ 'sources': [
+ u'woldlab_100826_HSI-123_0001_61MJTAAXX_l6_r1.tar.bz2'],
+ },
+ }
for args in qseq:
- args = extract_argument_list(args)
- expected = qseq_data[args[1]]
- self.failUnless(expected[0] in args[3])
- self.failUnless(expected[1] in args[5])
-
- split_data ={u'/notarealplace/11154_C02F9ACXX_c202_l3_r2.fastq':
- [u'11154_NoIndex_L003_R2_001.fastq.gz',
- u'11154_NoIndex_L003_R2_002.fastq.gz'],
- u'/notarealplace/11154_C02F9ACXX_c202_l3_r1.fastq':
- [u'11154_NoIndex_L003_R1_001.fastq.gz',
- u'11154_NoIndex_L003_R1_002.fastq.gz'],
- }
- for args in split:
- args = extract_argument_list(args)
- expected = split_data[args[1]]
- self.failUnless(expected[0] in args[2])
- self.failUnless(expected[1] in args[3])
+ expected = qseq_data[args['target']]
+ self.failUnlessEqual(args['istar'], expected['istar'])
+ self.failUnlessEqual(args['ispaired'], expected['ispaired'])
+ for i in range(len(expected['sources'])):
+ _, filename = os.path.split(args['sources'][i])
+ self.failUnlessEqual(filename, expected['sources'][i])
+
+
+ split_test = { x['target']: x for x in
+ [{'sources': [u'11154_NoIndex_L003_R1_001.fastq.gz',
+ u'11154_NoIndex_L003_R1_002.fastq.gz'],
+ 'pyscript': 'desplit_fastq.pyc',
+ 'target': u'11154_C02F9ACXX_c202_l3_r1.fastq'},
+ {'sources': [u'11154_NoIndex_L003_R2_001.fastq.gz',
+ u'11154_NoIndex_L003_R2_002.fastq.gz'],
+ 'pyscript': 'desplit_fastq.pyc',
+ 'target': u'11154_C02F9ACXX_c202_l3_r2.fastq'}]
+ }
+ for arg in split:
+ _, target = os.path.split(arg['target'])
+ pyscript = split_test[target]['pyscript']
+ self.failUnless(arg['pyscript'].endswith(pyscript))
+ filename = split_test[target]['target']
+ self.failUnless(arg['target'].endswith(filename))
+ for s_index in range(len(arg['sources'])):
+ s1 = arg['sources'][s_index]
+ s2 = split_test[target]['sources'][s_index]
+ self.failUnless(s1.endswith(s2))
#print '-------commands---------'
#pprint (commands)
-def extract_argument_list(condor_argument):
- args = condor_argument.split()
- # eat the command name, and the trailing queue
- return args[1:-1]
+ def test_create_scripts(self):
+ os.chdir(self.tempdir)
+ extract = condorfastq.CondorFastqExtract('host',
+ FAKE_APIDATA,
+ self.tempdir,
+ self.logdir)
+ extract.api = FakeApi()
+ result_map = [('11154', self.subname)]
+ extract.create_scripts(result_map)
+
+ self.failUnless(os.path.exists('srf.condor'))
+ with open('srf.condor', 'r') as srf:
+ arguments = [ l for l in srf if l.startswith('argument') ]
+ arguments.sort()
+ self.failUnlessEqual(len(arguments), 2)
+ self.failUnless('--single sub-11154/11154_30221AAXX_c33_l4.fastq'
+ in arguments[0])
+ self.failUnless(
+ '--right sub-11154/11154_30DY0AAXX_c151_l8_r2.fastq' in
+ arguments[1])
+
+ self.failUnless(os.path.exists('qseq.condor'))
+ with open('qseq.condor', 'r') as srf:
+ arguments = [ l for l in srf if l.startswith('argument') ]
+ arguments.sort()
+ self.failUnlessEqual(len(arguments), 3)
+ self.failUnless('-o sub-11154/11154_42JUYAAXX_c76_l5_r1.fastq ' in
+ arguments[0])
+ self.failUnless(
+ 'C1-76/woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2' in
+ arguments[1])
+ self.failUnless('61MJTAAXX_c76_l6.fastq -f 61MJTAAXX' in
+ arguments[2])
+
+ self.failUnless(os.path.exists('split_fastq.condor'))
+ with open('split_fastq.condor', 'r') as split:
+ arguments = [ l for l in split if l.startswith('argument') ]
+ arguments.sort()
+ self.failUnlessEqual(len(arguments), 2)
+ self.failUnless('11154_NoIndex_L003_R1_001.fastq.gz' in \
+ arguments[0])
+ self.failUnless('11154_NoIndex_L003_R2_002.fastq.gz' in \
+ arguments[1])
+
def suite():
suite = unittest.makeSuite(TestCondorFastq, 'test')
projects / htsworkflow.git / blobdiff