def load_mzml_file(files, start_time, stop_time):
"""Load MS1 scans from MZML files"""
t0 = timer.time()
ScanList = {}
ms1ScanList = {}
profiles = {}
for file_iter in files:
parser = mspy.parseMZML(path + file_iter + ".mzML")
parser.load()
ScanList[file_iter] = parser.scanlist()
ms1ScanList[file_iter] = []
profiles[file_iter] = {}
for key, scan_info in ScanList[file_iter].iteritems():
if (
scan_info["msLevel"] == 1
and scan_info["retentionTime"] >= start_time
and scan_info["retentionTime"] <= stop_time
):
ms1ScanList[file_iter].append(key)
profiles[file_iter][key] = parser.scan(key).profile
t1 = timer.time() - t0
print "Extracted data in %s " % t1
return [ScanList, ms1ScanList, profiles]
def load_mzml_file(self):
"""Load MS1 scans from MZML files"""
t0 = timer.time()
self.parser = mspy.parseMZML(self.filename + '.mzML')
self.parser.load()
self.scan_list = self.parser.scanlist()
self.ms1_indices = []
self.profiles = {}
for key, scan_info in self.scan_list.iteritems():
if scan_info['msLevel'] == 1 \
and scan_info['retentionTime'] >= self.start_time \
and scan_info['retentionTime'] <= self.stop_time:
self.ms1_indices.append(key)
self.profiles[key] = self.parser.scan(key).profile
t1 = timer.time() - t0
print 'Loaded MS1 spectra in %s ' % t1
def export_html():
tmpDir = ''
reportPath = os.path.join('test.html')
reportHTML=REPORT_HEADER
with open('d3.v3.min.js','r') as d3file:
reportHTML += d3file.read()
reportHTML += '</script>\n<body><div id="graph" class="aGraph" style="position:absolute;top:0px;left:0; float:left;"></div>'
mzfile = mspy.parseMZML('t0r3t1.mzML')
mzfile.load()
print 'Loaded MZML file'
scanlist = mzfile.scanlist()
relevant_scans_20 = []
for i_scan in scanlist.keys():
if scanlist[i_scan]['filterString'] == u'FTMS + p ESI sid=35.00 Full ms2 [email protected] [500.00-1600.00]' and scanlist[i_scan]['retentionTime'] > 300 and scanlist[i_scan]['retentionTime'] < 480:
relevant_scans_20.append(i_scan)
av_scan_20 = None
for i_scan in relevant_scans_20:
if av_scan_20 == None:
av_scan_20 = mzfile.scan(i_scan)
else:
av_scan_20 += mzfile.scan(i_scan)
av_scan_20.profile = mspy.filter(av_scan_20.profile, 0.002)
reportHTML += '<script>\ndata_x = ['
reportHTML += ','.join(map(str,av_scan_20.profile.T[0]))
reportHTML += '];\n'
reportHTML += 'data_y = ['
reportHTML += ','.join(map(str,av_scan_20.profile.T[1]))
reportHTML += '];\n'
reportHTML += GRAPH_SCRIPT
reportHTML += '</script>'
reportHTML += '</body>'
reportFile = file(reportPath, 'w')
reportFile.write(reportHTML.encode("utf-8"))
reportFile.close()
