def test_quick_index():
reader = ms_deisotope.MSFileLoader(mzml_path)
index, _interval_tree = quick_index.index(reader)
n_1 = len(index.ms1_ids)
n_n = len(index.msn_ids)
assert n_1 == 14
assert n_n == 34
def metadata_index(paths, processes=4):
'''Build an external scan metadata index for a mass spectrometry data file
This extended index is saved in a separate JSON file that can be loaded with
:class:`~.ExtendedScanIndex`. It includes the scan time of all scans, the precursor
mass of MSn scans, as well as the relationships between precursor and product ion
scans, as well as other details. See :class:`~.ExtendedScanIndex` for more information
'''
for path in paths:
reader = MSFileLoader(path)
try:
fn = reader.prebuild_byte_offset_file
if not reader.source._check_has_byte_offset_file():
fn(path)
except AttributeError:
pass
if processes > 1:
index, _ = quick_index.index(reader, processes)
else:
index = quick_index.ExtendedScanIndex()
reader.reset()
for bunch in reader:
index.add_scan_bunch(bunch)
name = path
index_file_name = index.index_file_name(name)
with open(index_file_name, 'w') as fh:
index.serialize(fh)
def metadata_index(paths, processes=4, deconvoluted=False):
'''Build an external scan metadata index for a mass spectrometry data file
This extended index is saved in a separate JSON file that can be loaded with
:class:`~.ExtendedScanIndex`. It includes the scan time of all scans, the precursor
mass of MSn scans, as well as the relationships between precursor and product ion
scans, as well as other details. See :class:`~.ExtendedScanIndex` for more information
'''
for path in paths:
click.echo("Indexing %s" % (path, ))
if deconvoluted:
reader = ProcessedMzMLDeserializer(path, use_extended_index=False)
else:
reader = MSFileLoader(path)
try:
fn = reader.prebuild_byte_offset_file
if not reader.source._check_has_byte_offset_file():
fn(path)
except AttributeError:
pass
if processes > 1:
progbar = progress(label='Building Index', length=100)
acc = [0]
def update_bar(x):
'''Progress Bar update callback for :func:`~.quick_index.index`
'''
x = int(x * 100)
x -= acc[0] # pylint: disable=cell-var-from-loop
progbar.update(x) # pylint: disable=cell-var-from-loop
acc[0] += x # pylint: disable=cell-var-from-loop
with progbar:
update_bar(0.0)
index, _ = quick_index.index(
reader, processes, progress_indicator=update_bar)
else:
index = quick_index.ExtendedScanIndex()
reader.reset()
try:
n = len(reader)
progbar = progress(label='Building Index', length=n)
except TypeError:
progbar = spinner(title="Building Index")
with progbar:
for bunch in reader.make_iterator(grouped=True):
i = 0
i += bunch.precursor is not None
i += len(bunch.products)
index.add_scan_bunch(bunch)
progbar.update(i)
name = path
index_file_name = index.index_file_name(name)
with open(index_file_name, 'w') as fh:
index.serialize(fh)
def metadata_index(paths, processes=4):
for path in paths:
reader = ms_deisotope.MSFileLoader(path)
try:
fn = reader.prebuild_byte_offset_file
if not reader.source._check_has_byte_offset_file():
fn(path)
except AttributeError:
pass
index, interval_tree = quick_index.index(reader, processes)
name = path
index_file_name = index.index_file_name(name)
with open(index_file_name, 'w') as fh:
index.serialize(fh)
def oxonium_signature(ms_file, g_score_threshold=0.05):
reader = ProcessedMzMLDeserializer(ms_file)
if not reader.has_index_file():
click.secho("Building temporary index...", fg='yellow')
index, intervals = quick_index.index(ms_deisotope.MSFileLoader(ms_file))
reader.extended_index = index
with open(reader._index_file_name, 'w') as handle:
index.serialize(handle)
from glycan_profiling.tandem.glycan.scoring.signature_ion_scoring import SignatureIonScorer
from glycan_profiling.tandem.oxonium_ions import gscore_scanner
refcomp = glypy.GlycanComposition.parse("{Fuc:1; Hex:5; HexNAc:4; Neu5Ac:2}")
for scan_id in reader.extended_index.msn_ids.keys():
scan = reader.get_scan_by_id(scan_id)
gscore = gscore_scanner(scan.deconvoluted_peak_set)
if gscore >= g_score_threshold:
signature_match = SignatureIonScorer.evaluate(scan, refcomp)
click.echo("%s\t%f\t%r\t%f\t%f" % (
scan_id, scan.precursor_information.neutral_mass,
scan.precursor_information.charge, gscore,
signature_match.score))
def msfile_info(ms_file):
reader = ProcessedMzMLDeserializer(ms_file)
if not reader.has_index_file():
index, intervals = quick_index.index(
ms_deisotope.MSFileLoader(ms_file))
reader.extended_index = index
with open(reader._index_file_name, 'w') as handle:
index.serialize(handle)
click.echo("Name: %s" % (os.path.basename(ms_file), ))
click.echo("MS1 Scans: %d" % (len(reader.extended_index.ms1_ids), ))
click.echo("MSn Scans: %d" % (len(reader.extended_index.msn_ids), ))
n_defaulted = 0
n_orphan = 0
charges = defaultdict(int)
first_msn = float('inf')
last_msn = 0
for scan_info in reader.extended_index.msn_ids.values():
n_defaulted += scan_info.get('defaulted', False)
n_orphan += scan_info.get('orphan', False)
charges[scan_info['charge']] += 1
rt = scan_info['scan_time']
if rt < first_msn:
first_msn = rt
if rt > last_msn:
last_msn = rt
click.echo("First MSn Scan: %0.2f Minutes" % (first_msn, ))
click.echo("Last MSn Scan: %0.2f Minutes" % (last_msn, ))
for charge, count in sorted(charges.items()):
if not isinstance(charge, int):
continue
click.echo("Precursors with Charge State %d: %d" % (charge, count))
click.echo("Defaulted MSn Scans: %d" % (n_defaulted, ))
click.echo("Orphan MSn Scans: %d" % (n_orphan, ))
def oxonium_signature(ms_file, g_score_threshold=0.05):
reader = ProcessedMzMLDeserializer(ms_file)
if not reader.has_index_file():
click.secho("Building temporary index...", fg='yellow')
index, intervals = quick_index.index(
ms_deisotope.MSFileLoader(ms_file))
reader.extended_index = index
with open(reader._index_file_name, 'w') as handle:
index.serialize(handle)
from glycan_profiling.tandem.glycan.scoring.signature_ion_scoring import SignatureIonScorer
from glycan_profiling.tandem.oxonium_ions import gscore_scanner
refcomp = glypy.GlycanComposition.parse(
"{Fuc:1; Hex:5; HexNAc:4; Neu5Ac:2}")
for scan_id in reader.extended_index.msn_ids.keys():
scan = reader.get_scan_by_id(scan_id)
gscore = gscore_scanner(scan.deconvoluted_peak_set)
if gscore >= g_score_threshold:
signature_match = SignatureIonScorer.evaluate(scan, refcomp)
click.echo("%s\t%f\t%r\t%f\t%f" %
(scan_id, scan.precursor_information.neutral_mass,
scan.precursor_information.charge, gscore,
signature_match.score))
def msfile_info(ms_file):
reader = ProcessedMzMLDeserializer(ms_file)
if not reader.has_index_file():
index, intervals = quick_index.index(ms_deisotope.MSFileLoader(ms_file))
reader.extended_index = index
with open(reader._index_file_name, 'w') as handle:
index.serialize(handle)
click.echo("Name: %s" % (os.path.basename(ms_file),))
click.echo("MS1 Scans: %d" % (len(reader.extended_index.ms1_ids),))
click.echo("MSn Scans: %d" % (len(reader.extended_index.msn_ids),))
n_defaulted = 0
n_orphan = 0
charges = defaultdict(int)
first_msn = float('inf')
last_msn = 0
for scan_info in reader.extended_index.msn_ids.values():
n_defaulted += scan_info.get('defaulted', False)
n_orphan += scan_info.get('orphan', False)
charges[scan_info['charge']] += 1
rt = scan_info['scan_time']
if rt < first_msn:
first_msn = rt
if rt > last_msn:
last_msn = rt
click.echo("First MSn Scan: %0.2f Minutes" % (first_msn,))
click.echo("Last MSn Scan: %0.2f Minutes" % (last_msn,))
for charge, count in sorted(charges.items()):
if not isinstance(charge, int):
continue
click.echo("Precursors with Charge State %d: %d" % (charge, count))
click.echo("Defaulted MSn Scans: %d" % (n_defaulted,))
click.echo("Orphan MSn Scans: %d" % (n_orphan,))
reader, lock = reader_index[path]
values = request.values
print(values)
with lock:
scan = reader.get_scan_by_id(scan_id)
response = format_scan(scan, values)
return response
if __name__ == "__main__":
import sys
for i, path in enumerate(sys.argv[1:]):
print("Loading {0} with Key {1}".format(path, i))
reader = MSFileLoader(path)
index_path = ExtendedScanIndex.index_file_name(path)
if os.path.exists(index_path):
file_index = ExtendedScanIndex.load(open(index_path, 'rt'))
else:
print("Indexing {0}".format(path))
reader.reset()
file_index, scan_tree = quick_index.index(reader)
reader.reset()
with open(index_path, 'wt') as fh:
file_index.dump(fh)
print(file_index)
metadata_index[path] = file_index
reader_index[path] = reader, RLock()
key_index[str(i)] = path
app.run(threaded=True)