def _init_iter(self):
if self.first_run_slice_bb is None:
raise StopIteration
self.curr_scan_slices = bb_to_scan_slices(
bytes(self.first_run_slice_bb.data), self.first_run_slice_bb.run_slice_id, self.reader.struct_by_scan_id)
while 1:
row = self.cursor.fetchone()
if row is None:
self.first_run_slice_bb = None
break
bb = BoundingBox._make(row)
if bb.run_slice_id == self.first_run_slice_bb.run_slice_id:
self.curr_scan_slices += bb_to_scan_slices(
bytes(bb.data), bb.run_slice_id, self.reader.struct_by_scan_id)
else:
self.first_run_slice_bb = bb
break
def get_xic(self, min_mz, max_mz, min_rt=0.0, max_rt=0.0, ms_level=1):
"""
eXtracted Ion Chromatogram
:param min_mz:
:param max_mz:
:param min_rt:
:param max_rt:
:param ms_level:
:return:
"""
min_mz_rs = self.run_slices_begin_mz[bisect_left(self.run_slices_begin_mz, min_mz) - 1]
max_mz_rs = self.run_slices_begin_mz[bisect_left(self.run_slices_begin_mz, max_mz) - 1]
# print "min max rs", min_mz_rs, max_mz_rs
if min_mz_rs == max_mz_rs:
sql_query = """SELECT bounding_box.id, data, run_slice_id, first_spectrum_id
FROM bounding_box, run_slice WHERE run_slice.ms_level = ?
AND bounding_box.run_slice_id = run_slice.id
AND run_slice.begin_mz = ?;"""
self.cursor.execute(sql_query, (ms_level, min_mz_rs))
else:
sql_query = """SELECT bounding_box.id, data, run_slice_id, first_spectrum_id
FROM bounding_box, run_slice WHERE run_slice.ms_level = ?
AND bounding_box.run_slice_id = run_slice.id
AND (run_slice.begin_mz = ? OR run_slice.begin_mz = ?);"""
self.cursor.execute(sql_query, (ms_level, min_mz_rs, max_mz_rs))
intensities_by_scan_time = ddict(int)
for row in self.cursor:
scan_slices = bb_to_scan_slices(row[1][:], row[2], self.struct_by_scan_id)
for ss in scan_slices:
time = self.rt_by_scan_id_by_ms_level[ms_level][ss.scan_id]
mzs = ss.mzs
min_idx = bisect_left(mzs, min_mz)
max_idx = bisect_left(mzs, max_mz)
ints = ss.ints[min_idx: max_idx]
if not ints:
continue
m = max(ints)
# if m > intensities_by_scan_time[time]:
intensities_by_scan_time[time] = m
times = sorted(intensities_by_scan_time.viewkeys())
intensities = [intensities_by_scan_time[t] for t in times]
return times, intensities
def get_scan(self, scan_id):
first_scan_id = self._get_bb_first_scan_id(scan_id)
print first_scan_id
sql_query = "SELECT id, data, run_slice_id FROM bounding_box WHERE bounding_box.first_spectrum_id = ?"
self.cursor.execute(sql_query, (first_scan_id,))
mzs, ints = [], []
for row in self.cursor:
scan_slices = bb_to_scan_slices(row[1][:], row[2], self.struct_by_scan_id)
for s in scan_slices:
if s.scan_id == scan_id:
mzs += s.mzs
ints += s.ints
break
return scan_id, mzs, ints