def test_metadata(self):
database: TestDatabase = TestDatabase()
table1: TestTable = database.create_table("table1")
entry1: TestEntry = table1.add_entry("0/123.4-13/1/1-1-1-test.mzML",
INPUT)
it = mzML.Iterator(entry1)
self.assertEqual(it.header_start_index, 0)
self.assertEqual(it.header_end_index, 122)
self.assertEqual(it.spectra_start_index, 123)
self.assertEqual(it.spectra_end_index, 734)
self.assertEqual(it.chromatogram_start_index, -1)
self.assertEqual(it.chromatogram_end_index, -1)
self.assertEqual(it.index_list_offset, 774)
self.assertEqual(it.footer_start_index, 735)
self.assertEqual(it.footer_end_index, len(entry1.get_content()))
entry2: TestEntry = table1.add_entry("0/123.4-13/1/1-1-1-ctest.mzML",
CHROMATOGRAM_INPUT)
it = mzML.Iterator(entry2)
self.assertEqual(it.header_start_index, 0)
self.assertEqual(it.header_end_index, 122)
self.assertEqual(it.spectra_start_index, 123)
self.assertEqual(it.spectra_end_index, 618)
self.assertEqual(it.chromatogram_start_index, 641)
self.assertEqual(it.chromatogram_end_index, 847)
self.assertEqual(it.index_list_offset, 890)
self.assertEqual(it.footer_start_index, 619)
self.assertEqual(it.footer_end_index, len(entry2.get_content()))
def test_adjust(self):
database: TestDatabase = TestDatabase()
table1: TestTable = database.create_table("table1")
entry1: TestEntry = table1.add_entry("0/123.4-13/1/1-1-1-test.mzML",
INPUT)
# Multiple spectra start in range
it = mzML.Iterator(entry1, OffsetBounds(120, 540))
[spectra, offset_bounds, more] = it.next()
self.assertFalse(more)
self.assertEqual(offset_bounds.start_index, 123)
self.assertEqual(offset_bounds.end_index, 733)
self.assertEqual(len(list(spectra)), 3)
# One spectra starts in range
it = mzML.Iterator(entry1, OffsetBounds(120, 250))
[spectra, offset_bounds, more] = it.next()
self.assertFalse(more)
self.assertEqual(offset_bounds.start_index, 123)
self.assertEqual(offset_bounds.end_index, 320)
# No spectra start in range
it = mzML.Iterator(entry1, OffsetBounds(126, 240))
[spectra, offset_bounds, more] = it.next()
self.assertFalse(more)
self.assertEqual(offset_bounds.start_index, 123)
self.assertEqual(offset_bounds.end_index, 320)
def test_identifier(self):
database: TestDatabase = TestDatabase()
table1: TestTable = database.create_table("table1")
entry1: TestEntry = table1.add_entry("0/123.4-13/1/1-1-1-test.mzML",
INPUT)
it = mzML.Iterator(entry1)
[items, offset_bounds, more] = it.next()
spectra = list(items)
self.assertEqual(
it.get_identifier_value(spectra[0], mzML.Identifiers.mass), 123.0)
self.assertEqual(
it.get_identifier_value(spectra[1], mzML.Identifiers.mass), 4.0)
self.assertEqual(
it.get_identifier_value(spectra[2], mzML.Identifiers.mass), 566.0)
def test_next(self):
database: TestDatabase = TestDatabase()
table1: TestTable = database.create_table("table1")
entry1: TestEntry = table1.add_entry("0/123.4-13/1/1-1-1-test.mzML",
INPUT)
it = mzML.Iterator(entry1)
[spectra, offset_bounds, more] = it.next()
spectra = list(spectra)
self.assertFalse(more)
self.assertEqual(len(spectra), 3)
self.assertEqual(spectra[0].get("id"),
"controllerType=0 controllerNumber=1 scan=1")
self.assertEqual(spectra[1].get("id"),
"controllerType=0 controllerNumber=1 scan=2")
self.assertEqual(spectra[2].get("id"),
"controllerType=0 controllerNumber=1 scan=3")
def create_spectra_file(name, num_spectra):
spectra = []
# name = "10sep2013_yeast_control_1.mzML"
s3 = S3({})
bucket_name = "tide-source-data"
objs = s3.get_entries(bucket_name, "Coon-SingleShotFusionYeast/" + name)
for obj in objs:
if len(spectra) < num_spectra:
it = mzML.Iterator(obj)
extra = it.get_extra()
more = True
while len(spectra) < num_spectra and more:
[items, _, more] = it.next()
items = list(items)
print(len(spectra), len(items))
add_count = min(len(items), num_spectra - len(spectra))
spectra += items[:add_count]
else:
break
with open(name, "wb+") as f:
it.from_array(spectra, f, extra)