import os
import shutil
import tempfile
-import unittest
+from unittest import TestCase
-from htsworkflow.pipelines import sequences
+import RDF
+from htsworkflow.pipelines import sequences
+from htsworkflow.util.rdfhelp import get_model, load_string_into_model, \
+ rdfNS, libraryOntology, dump_model, fromTypedNode
-class SequenceFileTests(unittest.TestCase):
+class SequenceFileTests(TestCase):
"""
Make sure the sequence archive class works
"""
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<srf 42BW9AAXX 4 %s>" % (pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, None)
self.assertEqual(f0.pf, None)
self.assertEqual(f0.cycle, 38)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<qseq 42BW9AAXX 4 %s>" %(pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, None)
self.assertEqual(f0.cycle, 36)
self.assertEqual(f0.path, pathname)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<qseq ilmn200901 1 %s>" %(pathname,))
- self.assertEqual(f0.lane, 1)
+ self.assertEqual(f0.lane, '1')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, None)
self.assertEqual(f0.cycle, 202)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" % (pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, True)
self.assertEqual(f0.cycle, 38)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" %(pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 4)
+ self.assertEqual(f0.lane, '4')
self.assertEqual(f0.read, 2)
self.assertEqual(f0.pf, False)
self.assertEqual(f0.cycle, 38)
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" %(pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 1)
+ self.assertEqual(f0.lane, '1')
self.assertEqual(f0.read, 1)
self.assertEqual(f0.pf, True)
self.assertEqual(f0.project, '11111')
self.assertEqual(unicode(f0), unicode(pathname))
self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" % (pathname,))
self.assertEqual(f0.flowcell, '42BW9AAXX')
- self.assertEqual(f0.lane, 1)
+ self.assertEqual(f0.lane, '1')
self.assertEqual(f0.read, 2)
self.assertEqual(f0.pf, True)
self.assertEqual(f0.project, '11112')
self.assertEqual(f.filetype, 'eland')
self.assertEqual(f.path, pathname)
self.assertEqual(f.flowcell, '42BW9AAXX')
- self.assertEqual(f.lane, 4)
+ self.assertEqual(f.lane, '4')
self.assertEqual(f.read, None)
self.assertEqual(f.pf, None)
self.assertEqual(f.cycle, 38)
self.assertEqual(f.filetype, 'eland')
self.assertEqual(f.path, pathname)
self.assertEqual(f.flowcell, '42BW9AAXX')
- self.assertEqual(f.lane, 4)
+ self.assertEqual(f.lane, '4')
self.assertEqual(f.read, 1)
self.assertEqual(f.pf, None)
self.assertEqual(f.cycle, 152)
self.assertEqual(f.make_target_name('/tmp'),
'/tmp/42BW9AAXX_152_s_4_1_eland_extended.txt.bz2')
- def test_sql(self):
- """
- Make sure that the quick and dirty sql interface in sequences works
- """
- import sqlite3
- db = sqlite3.connect(":memory:")
- c = db.cursor()
- sequences.create_sequence_table(c)
-
+ def _generate_sequences(self):
+ seqs = []
data = [('/root/42BW9AAXX/C1-152',
'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l1_r1.tar.bz2'),
('/root/42BW9AAXX/C1-152',
'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l2_r21.tar.bz2'),]
for path, name in data:
- seq = sequences.parse_qseq(path, name)
- seq.save(c)
+ seqs.append(sequences.parse_qseq(path, name))
+
+ path = '/root/42BW9AAXX/C1-38/Project_12345'
+ name = '12345_AAATTT_L003_R1_001.fastq.gz'
+ pathname = os.path.join(path,name)
+ seqs.append(sequences.parse_fastq(path, name))
+ self.assertEqual(len(seqs), 5)
+ return seqs
+
+
+ def test_sql(self):
+ """
+ Make sure that the quick and dirty sql interface in sequences works
+ """
+ import sqlite3
+ db = sqlite3.connect(":memory:")
+ c = db.cursor()
+ sequences.create_sequence_table(c)
+
+ for seq in self._generate_sequences():
+ seq.save_to_sql(c)
count = c.execute("select count(*) from sequences")
row = count.fetchone()
- self.assertEqual(row[0], 4)
+ self.assertEqual(row[0], 5)
+
+ def test_basic_rdf_scan(self):
+ """Make sure we can save to RDF model"""
+ import RDF
+ model = get_model()
+
+ for seq in self._generate_sequences():
+ seq.save_to_model(model)
+
+ files = list(model.find_statements(
+ RDF.Statement(None,
+ rdfNS['type'],
+ libraryOntology['IlluminaResult'])))
+ self.assertEqual(len(files), 5)
+ files = list(model.find_statements(
+ RDF.Statement(None,
+ libraryOntology['file_type'],
+ libraryOntology['qseq'])))
+ self.assertEqual(len(files), 4)
+ files = list(model.find_statements(
+ RDF.Statement(None,
+ libraryOntology['file_type'],
+ libraryOntology['split_fastq'])))
+ self.assertEqual(len(files), 1)
+
+ files = list(model.find_statements(
+ RDF.Statement(None, libraryOntology['library_id'], None)))
+ self.assertEqual(len(files), 1)
+
+ files = list(model.find_statements(
+ RDF.Statement(None, libraryOntology['flowcell_id'], None)))
+ self.assertEqual(len(files), 5)
+
+ files = list(model.find_statements(
+ RDF.Statement(None, libraryOntology['flowcell'], None)))
+ self.assertEqual(len(files), 0)
+
+ files = list(model.find_statements(
+ RDF.Statement(None, libraryOntology['library'], None)))
+ self.assertEqual(len(files), 0)
+
+ def test_rdf_scan_with_url(self):
+ """Make sure we can save to RDF model"""
+ import RDF
+ model = get_model()
+ base_url = 'http://localhost'
+ for seq in self._generate_sequences():
+ seq.save_to_model(model, base_url=base_url)
+ localFC = RDF.NS(base_url + '/flowcell/')
+ localLibrary = RDF.NS(base_url + '/library/')
+
+ files = list(model.find_statements(
+ RDF.Statement(None, libraryOntology['flowcell'], None)))
+ self.assertEqual(len(files), 5)
+ for f in files:
+ self.assertEqual(f.object, localFC['42BW9AAXX/'])
+
+ files = list(model.find_statements(
+ RDF.Statement(None, libraryOntology['library'], None)))
+ self.assertEqual(len(files), 1)
+ self.assertEqual(files[0].object, localLibrary['12345'])
+
+ def test_rdf_fixup_library(self):
+ """Make sure we can save to RDF model"""
+ base_url = 'http://localhost'
+ localLibrary = RDF.NS(base_url + '/library/')
+
+ flowcellInfo = """@prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
+
+<{base}/flowcell/42BW9AAXX/>
+ libns:flowcell_id "42BW9AXX"@en ;
+ libns:has_lane <{base}/lane/1169>, <{base}/lane/1170>,
+ <{base}/lane/1171>, <{base}/lane/1172> ;
+ libns:read_length 75 ;
+ a libns:IlluminaFlowcell .
+
+<{base}/lane/1169>
+ libns:lane_number "1" ; libns:library <{base}/library/10923/> .
+<{base}/lane/1170>
+ libns:lane_number "2" ; libns:library <{base}/library/10924/> .
+<{base}/lane/1171>
+ libns:lane_number "3" ; libns:library <{base}/library/12345/> .
+<{base}/lane/1172>
+ libns:lane_number "3" ; libns:library <{base}/library/10930/> .
+""".format(base=base_url)
+ model = get_model()
+ load_string_into_model(model, 'turtle', flowcellInfo)
+ for seq in self._generate_sequences():
+ seq.save_to_model(model)
+ f = sequences.update_model_sequence_library(model, base_url=base_url)
+
+ libTerm = libraryOntology['library']
+ libIdTerm = libraryOntology['library_id']
+
+ url = 'file:///root/42BW9AAXX/C1-152/woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l1_r2.tar.bz2'
+ nodes = list(model.get_targets(RDF.Uri(url), libTerm))
+ self.assertEqual(len(nodes), 1)
+ self.assertEqual(nodes[0], localLibrary['10923/'])
+ nodes = list(model.get_targets(RDF.Uri(url), libIdTerm))
+ self.assertEqual(len(nodes), 1)
+ self.assertEqual(fromTypedNode(nodes[0]), '10923')
+
+ url = 'file:///root/42BW9AAXX/C1-152/woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l2_r1.tar.bz2'
+ nodes = list(model.get_targets(RDF.Uri(url), libTerm))
+ self.assertEqual(len(nodes), 1)
+ self.assertEqual(nodes[0], localLibrary['10924/'])
+ nodes = list(model.get_targets(RDF.Uri(url), libIdTerm))
+ self.assertEqual(len(nodes), 1)
+ self.assertEqual(fromTypedNode(nodes[0]), '10924')
+
+ url = 'file:///root/42BW9AAXX/C1-38/Project_12345/12345_AAATTT_L003_R1_001.fastq.gz'
+ nodes = list(model.get_targets(RDF.Uri(url), libTerm))
+ self.assertEqual(len(nodes), 1)
+ self.assertEqual(nodes[0], localLibrary['12345/'])
+ nodes = list(model.get_targets(RDF.Uri(url), libIdTerm))
+ self.assertEqual(len(nodes), 1)
+ self.assertEqual(fromTypedNode(nodes[0]), '12345')
+
+ def test_load_from_model(self):
+ """Can we round trip through a RDF model"""
+ model = get_model()
+ path = '/root/42BW9AAXX/C1-38/Project_12345/'
+ filename = '12345_AAATTT_L003_R1_001.fastq.gz'
+ seq = sequences.parse_fastq(path, filename)
+ seq.save_to_model(model)
+
+ seq_id = 'file://'+path+filename
+ seqNode = RDF.Node(RDF.Uri(seq_id))
+ libNode = RDF.Node(RDF.Uri('http://localhost/library/12345'))
+ model.add_statement(
+ RDF.Statement(seqNode, libraryOntology['library'], libNode))
+ seq2 = sequences.SequenceFile.load_from_model(model, seq_id)
+
+ self.assertEqual(seq.flowcell, seq2.flowcell)
+ self.assertEqual(seq.flowcell, '42BW9AAXX')
+ self.assertEqual(seq.filetype, seq2.filetype)
+ self.assertEqual(seq2.filetype, 'split_fastq')
+ self.assertEqual(seq.lane, seq2.lane)
+ self.assertEqual(seq2.lane, '3')
+ self.assertEqual(seq.read, seq2.read)
+ self.assertEqual(seq2.read, 1)
+ self.assertEqual(seq.project, seq2.project)
+ self.assertEqual(seq2.project, '12345')
+ self.assertEqual(seq.index, seq2.index)
+ self.assertEqual(seq2.index, 'AAATTT')
+ self.assertEqual(seq.split, seq2.split)
+ self.assertEqual(seq2.split, '001')
+ self.assertEqual(seq.cycle, seq2.cycle)
+ self.assertEqual(seq.pf, seq2.pf)
+ self.assertEqual(seq2.libraryNode, libNode)
+ self.assertEqual(seq.path, seq2.path)
def test_scan_for_sequences(self):
# simulate tree
file_types_seen = set()
file_types_to_see = set(['fastq', 'srf', 'eland', 'qseq'])
lanes = set()
- lanes_to_see = set((1,2,3))
+ lanes_to_see = set(('1','2','3'))
with SimulateSimpleTree() as tree:
seqs = sequences.scan_for_sequences([tree.root, '/a/b/c/98345'])
for s in seqs:
file_types_seen = set()
file_types_to_see = set(['split_fastq'])
lanes = set()
- lanes_to_see = set((1,2))
+ lanes_to_see = set(('1','2'))
projects_seen = set()
projects_to_see = set(('11111', '21111', '31111'))
with SimulateHiSeqTree() as tree:
def suite():
- return unittest.makeSuite(SequenceFileTests,'test')
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests))
+ return suite
+
if __name__ == "__main__":
- unittest.main(defaultTest="suite")
+ from unittest import main
+ main(defaultTest="suite")
projects / htsworkflow.git / blobdiff