| 1 |
nje01 |
1.1 |
#!/usr/bin/env python |
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import sys,os,os.path |
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import re |
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import sha |
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import math |
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import tempfile |
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import csv |
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import gzip |
| 10 |
nje01 |
1.3 |
import zlib |
| 11 |
nje01 |
1.1 |
from array import array |
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from base64 import b64encode,b64decode |
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from urllib import quote,unquote |
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from xml.sax import * |
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class NameVersion: |
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def __init__(self): |
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self.name_ = "PyMsXML" |
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self.majorVer = 0 |
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nje01 |
1.3 |
self.minorVer = 5 |
| 21 |
nje01 |
1.5 |
self.revVer = 2 |
| 22 |
nje01 |
1.1 |
def version(self): |
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return "%d.%d.%d"%(self.majorVer,self.minorVer,self.revVer) |
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def name(self): |
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return self.name_ |
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def fileSHA(filename): |
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s = sha.new() |
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h = open(filename,'rb') |
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while True: |
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buffer = h.read(1024) |
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if buffer == '': |
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break |
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s.update(buffer) |
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h.close() |
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return s.hexdigest().lower() |
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| 38 |
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class ToMzXML: |
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nje01 |
1.3 |
def __init__(self,reader,filename,cmpfmt=None,filt=None,peaksCompress=False,version="3.0"): |
| 40 |
nje01 |
1.1 |
self.filename = filename |
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self.compressfmt = cmpfmt |
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self.reader = reader |
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self.initSHA() |
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self.writeByteCounter = 0 |
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self.actualScanCount = 0 |
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self.scanIndices = {} |
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self.filter = filt |
| 48 |
nje01 |
1.3 |
if not version in ('2.1','2.2','3.0'): |
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raise "Bad mzXML version \"%s\""%(version,) |
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self.version = version |
| 51 |
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if peaksCompress and float(self.version) < 3.0: |
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raise "Cannot compress peaks until mzXML version 3.0" |
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self.peakcompress = peaksCompress |
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nje01 |
1.1 |
|
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def __del__(self): |
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if hasattr(self,'tmpFileName') and self.tmpFileName and self.tmpFileName != '': |
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os.unlink(self.tmpFileName) |
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def getFilename(self): |
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return self.filename |
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def initSHA(self): |
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self.sha1 = sha.new() |
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def updateSHA(self,s): |
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self.sha1.update(s) |
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def getSHA(self): |
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return self.sha1.hexdigest().lower() |
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def writeString(self,fh,data): |
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self.writeByteCounter += len(data) |
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self.sha1.update(data) |
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fh.write(data) |
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def write(self,debug=False): |
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# Make a temporary file for the scan data to count the number of spectra. |
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(tmpFileFD,self.tmpFileName) = tempfile.mkstemp(dir='.',prefix='.pymsxml') |
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tmpFile = os.fdopen(tmpFileFD,'wb') |
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# Has a number of side effects, it fills in scanIndices, and sets self.actualScanCount. |
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self.write_scans(tmpFile,debug) |
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tmpFile.close() |
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# Reset! |
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self.initSHA() |
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self.writeByteCounter = 0 |
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| 92 |
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if self.compressfmt == None and not self.filename.endswith('.gz'): |
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xmlFile = open(self.filename,'wb') |
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elif self.compressfmt == 'gz' or self.filename.endswith('.gz'): |
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if self.filename.endswith('.gz'): |
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xmlFile = gzip.open(self.filename,'wb') |
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else: |
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xmlFile = gzip.open(self.filename+'.gz','wb') |
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else: |
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print >>sys.stderr, "Bad compressfmt specification" |
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sys.exit(1) |
| 102 |
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| 103 |
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self.writeString (xmlFile,'<?xml version="1.0" encoding="ISO-8859-1"?>\n') |
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| 105 |
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outStr = "<mzXML " |
| 106 |
nje01 |
1.3 |
outStr += "xmlns=\"http://sashimi.sourceforge.net/schema_revision/mzXML_%s\" "%(self.version,) |
| 107 |
nje01 |
1.1 |
outStr += "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" " |
| 108 |
nje01 |
1.3 |
outStr += "xsi:schemaLocation=\"http://sashimi.sourceforge.net/schema_revision/mzXML_%s http://sashimi.sourceforge.net/schema_revision/mzXML_%s/mzXML_idx_%s.xsd\""%(self.version,self.version,self.version) |
| 109 |
nje01 |
1.1 |
outStr += ">\n" |
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| 111 |
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self.writeString (xmlFile,outStr) |
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| 113 |
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outStr = "<msRun" |
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outStr += " scanCount=\"%d\"" % (self.actualScanCount,) |
| 115 |
nje01 |
1.3 |
md = self.reader.getMsRunMetaData() |
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for (k,v) in md.items(): |
| 117 |
nje01 |
1.1 |
k,f = k.split(':') |
| 118 |
nje01 |
1.3 |
if self.version not in ('2.2',) or (k != 'startTime'and k != 'endTime'): |
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outStr += (" %%s=\"%s\""%(f,))%(k,v) |
| 120 |
nje01 |
1.1 |
outStr += ">\n" |
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| 122 |
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self.writeString (xmlFile,outStr) |
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| 124 |
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filehashes = {} |
| 125 |
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| 126 |
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for f in self.reader.getFilenames(): |
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if len(f) == 2: |
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outStr = "<parentFile " |
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outStr += "fileName=\"%s\" " % (quote(f[0]),) |
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outStr += "fileType=\"RAWData\" " |
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outStr += "fileSha1=\"%s\"" % (f[1],) |
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outStr += "/>\n" |
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else: |
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outStr = "<parentFile " |
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outStr += "fileName=\"%s\" " % (f[0],) |
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outStr += "fileType=\"%s\" " % (f[1],) |
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outStr += "fileSha1=\"%s\"" % (f[2],) |
| 138 |
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outStr += "/>\n" |
| 139 |
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self.writeString (xmlFile,outStr) |
| 140 |
nje01 |
1.3 |
|
| 141 |
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if float(self.version) >= 3.0: |
| 142 |
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outStr = "<msInstrument msInstrumentID=\"%s\">\n" % (self.reader.msInstrumentID(),) |
| 143 |
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else: |
| 144 |
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outStr = "<msInstrument>\n" |
| 145 |
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| 146 |
nje01 |
1.1 |
outStr += "<msManufacturer category=\"msManufacturer\" value=\"%s\"/>\n" % (self.reader.msManufacturer(),) |
| 147 |
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outStr += "<msModel category=\"msModel\" value=\"%s\"/>\n" % (self.reader.msModel(),) |
| 148 |
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if self.reader.msIonisation(): |
| 149 |
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outStr += "<msIonisation category=\"msIonisation\" value=\"%s\"/>\n" % (self.reader.msIonisation(),) |
| 150 |
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if self.reader.msMassAnalyzer(): |
| 151 |
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outStr += "<msMassAnalyzer category=\"msMassAnalyzer\" value=\"%s\"/>\n" % (self.reader.msMassAnalyzer(),) |
| 152 |
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if self.reader.msDetector(): |
| 153 |
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outStr += "<msDetector category=\"msDetector\" value=\"%s\"/>\n" % (self.reader.msDetector(),) |
| 154 |
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| 155 |
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self.writeString (xmlFile,outStr) |
| 156 |
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| 157 |
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outStr = "<software " |
| 158 |
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outStr += "type=\"acquisition\" " |
| 159 |
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outStr += "name=\"%s\" "%(self.reader.acquisitionSoftware(),) |
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outStr += "version=\"%s\""%(self.reader.acquisitionSoftwareVersion(),) |
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outStr += "/>\n" |
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self.writeString (xmlFile,outStr) |
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| 165 |
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outStr = "</msInstrument>\n" |
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| 167 |
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self.writeString (xmlFile,outStr) |
| 168 |
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| 169 |
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outStr = "<dataProcessing>\n" |
| 170 |
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| 171 |
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self.writeString (xmlFile,outStr) |
| 172 |
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| 173 |
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nv = NameVersion() |
| 174 |
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| 175 |
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outStr = "<software " |
| 176 |
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outStr += "type=\"conversion\" " |
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outStr += "name=\"%s\" "%(nv.name(),) |
| 178 |
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outStr += "version=\"%s\"" % (nv.version(),) |
| 179 |
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outStr += "/>\n" |
| 180 |
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| 181 |
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self.writeString (xmlFile,outStr) |
| 182 |
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| 183 |
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if (self.reader.peakDetect(1)): |
| 184 |
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outStr = "<processingOperation " |
| 185 |
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outStr += "name=\"peak_detection_level_1\" " |
| 186 |
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outStr += "value=\"true\"" |
| 187 |
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outStr += "/>\n" |
| 188 |
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outStr += "<processingOperation " |
| 189 |
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outStr += "name=\"peak_detection_level_1_threshold\" " |
| 190 |
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outStr += "value=\"1%\"" |
| 191 |
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outStr += "/>\n" |
| 192 |
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outStr += "<processingOperation " |
| 193 |
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outStr += "name=\"peak_detection_level_1_software\" " |
| 194 |
nje01 |
1.3 |
outStr += "value=\"%s\""%(self.reader.acquisitionSoftware(),) |
| 195 |
nje01 |
1.1 |
outStr += "/>\n" |
| 196 |
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self.writeString (xmlFile,outStr) |
| 197 |
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if (self.reader.peakDetect(2)): |
| 198 |
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outStr = "<processingOperation " |
| 199 |
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outStr += "name=\"peak_detection_level_2\" " |
| 200 |
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outStr += "value=\"true\"" |
| 201 |
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outStr += "/>\n" |
| 202 |
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outStr += "<processingOperation " |
| 203 |
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outStr += "name=\"peak_detection_level_2_threshold\" " |
| 204 |
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outStr += "value=\"1%\"" |
| 205 |
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outStr += "/>\n" |
| 206 |
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outStr += "<processingOperation " |
| 207 |
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outStr += "name=\"peak_detection_level_2_software\" " |
| 208 |
nje01 |
1.3 |
outStr += "value=\"%s\""%(self.reader.acquisitionSoftware(),) |
| 209 |
nje01 |
1.1 |
outStr += "/>\n" |
| 210 |
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self.writeString (xmlFile,outStr) |
| 211 |
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| 212 |
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outStr = "<processingOperation " |
| 213 |
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outStr += "name=\"min_peaks_per_spectra\" " |
| 214 |
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outStr += "value=\"1\"" |
| 215 |
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outStr += "/>\n" |
| 216 |
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| 217 |
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self.writeString (xmlFile,outStr) |
| 218 |
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| 219 |
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outStr = "</dataProcessing>\n" |
| 220 |
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| 221 |
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self.writeString (xmlFile,outStr) |
| 222 |
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| 223 |
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if self.reader.maldi(): |
| 224 |
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outStr = '<spotting>\n' |
| 225 |
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for d in self.reader.plateData(): |
| 226 |
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outStr += '<plate plateID="%s" spotXCount="%s" spotYCount="%s">\n' % \ |
| 227 |
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(d['plateID'],d['spotXCount'],d['spotYCount']) |
| 228 |
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outStr += '<plateManufacturer category="plateManufacturer" value="%s"/>\n' % \ |
| 229 |
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(d['plateManufacturer'],) |
| 230 |
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outStr += '<plateModel category="plateModel" value="%s"/>\n' % \ |
| 231 |
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(d['plateModel'],) |
| 232 |
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for s in self.reader.spotData(d['plateID']): |
| 233 |
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outStr += '<spot spotID="%s" spotXPosition="%s" spotYPosition="%s">\n' % \ |
| 234 |
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(s['spotID'],s['spotXPosition'],s['spotYPosition']) |
| 235 |
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outStr += '<maldiMatrix category="maldiMatrix" value="%s"/>\n' % \ |
| 236 |
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(s['maldiMatrix'],) |
| 237 |
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outStr += '</spot>\n' |
| 238 |
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outStr += '</plate>\n' |
| 239 |
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outStr += '</spotting>\n' |
| 240 |
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self.writeString(xmlFile,outStr) |
| 241 |
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| 242 |
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if self.reader.lc(): |
| 243 |
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pass |
| 244 |
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| 245 |
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scanOffset = self.writeByteCounter |
| 246 |
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| 247 |
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tmpFile = open(self.tmpFileName,'rb') |
| 248 |
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while True: |
| 249 |
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tmpStr = tmpFile.read(1024) |
| 250 |
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if tmpStr == '': |
| 251 |
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break |
| 252 |
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self.writeString(xmlFile,tmpStr) |
| 253 |
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tmpFile.close() |
| 254 |
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os.unlink(self.tmpFileName) |
| 255 |
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self.tmpFileName = '' |
| 256 |
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| 257 |
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outStr = "</msRun>\n" |
| 258 |
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self.writeString (xmlFile,outStr) |
| 259 |
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| 260 |
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indexOffset = self.writeByteCounter |
| 261 |
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| 262 |
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outStr = "<index " |
| 263 |
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outStr += "name=\"scan\" " |
| 264 |
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outStr += ">\n" |
| 265 |
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| 266 |
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self.writeString (xmlFile,outStr) |
| 267 |
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| 268 |
|
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for i in xrange(1,self.actualScanCount+1): |
| 269 |
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outStr = "<offset id=\"%d\">" % (i,) |
| 270 |
|
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outStr += "%d</offset>\n" % (self.scanIndices[i] + scanOffset,) |
| 271 |
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self.writeString(xmlFile,outStr) |
| 272 |
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| 273 |
|
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outStr = "</index>\n" |
| 274 |
|
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self.writeString (xmlFile,outStr) |
| 275 |
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| 276 |
|
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outStr = "<indexOffset>%d</indexOffset>\n" % (indexOffset,) |
| 277 |
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| 278 |
|
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self.writeString (xmlFile,outStr) |
| 279 |
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| 280 |
|
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self.writeString (xmlFile,"<sha1>") |
| 281 |
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| 282 |
|
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outStr = self.getSHA() |
| 283 |
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| 284 |
|
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self.writeString (xmlFile,outStr) |
| 285 |
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| 286 |
|
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self.writeString (xmlFile,"</sha1>\n") |
| 287 |
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| 288 |
|
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outStr = "</mzXML>\n" |
| 289 |
|
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self.writeString (xmlFile,outStr) |
| 290 |
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| 291 |
|
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xmlFile.close() |
| 292 |
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| 293 |
|
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def write_scans(self,xmlFile,debug=False): |
| 294 |
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| 295 |
|
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msLevel = 0 |
| 296 |
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scanNumber = 0 |
| 297 |
|
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ancestors = [] |
| 298 |
|
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self.writeByteCounter = 0 |
| 299 |
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| 300 |
|
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for (s,d) in self.reader.spectra(): |
| 301 |
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| 302 |
|
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if self.filter != None and not self.filter.test(d): |
| 303 |
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continue |
| 304 |
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| 305 |
|
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if debug and scanNumber >= 10: |
| 306 |
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break |
| 307 |
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| 308 |
|
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if not d.has_key('msLevel'): |
| 309 |
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print >>sys.stderr, "Required scan attributes missing." |
| 310 |
|
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sys.exit(1) |
| 311 |
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| 312 |
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prevLevel = msLevel |
| 313 |
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msLevel = d['msLevel'] |
| 314 |
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| 315 |
|
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if prevLevel < msLevel and prevLevel > 0: |
| 316 |
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# We went "in" a level, push scan number of parent |
| 317 |
|
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ancestors.append((scanNumber,prevSpec)) |
| 318 |
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elif prevLevel > msLevel and msLevel > 0: |
| 319 |
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if len(ancestors) == 0: |
| 320 |
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pass #print >>sys.stderr, "No ancestor for scan %s at level %s"%(scanNumber,msLevel) |
| 321 |
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else: |
| 322 |
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ancestors.pop() |
| 323 |
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| 324 |
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outStr = '' |
| 325 |
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if prevLevel > msLevel: |
| 326 |
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for m in xrange(0,prevLevel-msLevel+1): |
| 327 |
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outStr += "</scan>\n" |
| 328 |
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else: |
| 329 |
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if prevLevel > 0 and prevLevel == msLevel: |
| 330 |
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outStr += "</scan>\n" |
| 331 |
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| 332 |
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self.writeString(xmlFile,outStr) |
| 333 |
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| 334 |
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scanNumber = scanNumber + 1 |
| 335 |
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| 336 |
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self.scanIndices[scanNumber] = self.writeByteCounter |
| 337 |
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| 338 |
|
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totIonCurrent = 0 |
| 339 |
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maxmz = None |
| 340 |
|
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minmz = None |
| 341 |
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basePeakMz = None |
| 342 |
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basePeakIntensity = None |
| 343 |
|
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peaksCount = 0 |
| 344 |
|
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for i in xrange(0,len(s),2): |
| 345 |
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x = s[i]; y = s[i+1] |
| 346 |
|
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if minmz is None or minmz > x: |
| 347 |
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minmz = x |
| 348 |
|
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if maxmz is None or maxmz < x: |
| 349 |
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maxmz = x |
| 350 |
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totIonCurrent += y |
| 351 |
|
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if basePeakIntensity is None or basePeakIntensity < y: |
| 352 |
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basePeakIntensity = y |
| 353 |
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basePeakMz = x |
| 354 |
|
|
peaksCount += 1 |
| 355 |
|
|
|
| 356 |
|
|
outStr = "<scan num=\"%d\" msLevel=\"%d\"" % (scanNumber,msLevel) |
| 357 |
|
|
outStr += " peaksCount=\"%d\"" % (peaksCount,) |
| 358 |
|
|
outStr += " lowMz=\"%f\"" % (minmz,) |
| 359 |
|
|
outStr += " highMz=\"%f\"" % (maxmz,) |
| 360 |
|
|
outStr += " totIonCurrent=\"%f\"" % (totIonCurrent,) |
| 361 |
|
|
outStr += " basePeakMz=\"%f\"" % (basePeakMz,) |
| 362 |
|
|
outStr += " basePeakIntensity=\"%f\"" % (basePeakIntensity,) |
| 363 |
|
|
|
| 364 |
|
|
for (k,v) in d.items(): |
| 365 |
|
|
if k.startswith('scan.'): |
| 366 |
|
|
k,f = k.split(':') |
| 367 |
|
|
k = k[5:] |
| 368 |
|
|
outStr += (" %%s=\"%s\""%(f,))%(k,v) |
| 369 |
|
|
outStr += ">\n" |
| 370 |
|
|
self.writeString(xmlFile,outStr) |
| 371 |
|
|
|
| 372 |
nje01 |
1.3 |
if self.version in ('2.2',): |
| 373 |
|
|
any = False |
| 374 |
|
|
for (k,v) in d.items(): |
| 375 |
|
|
if k.startswith('scanOrigin.'): |
| 376 |
|
|
if not any: |
| 377 |
|
|
any = True |
| 378 |
|
|
outStr = "<scanOrigin" |
| 379 |
|
|
k,f = k.split(':') |
| 380 |
|
|
k = k[11:] |
| 381 |
|
|
outStr += (" %%s=\"%s\""%(f,))%(k,v) |
| 382 |
|
|
if any: |
| 383 |
|
|
outStr += "/>\n" |
| 384 |
|
|
self.writeString(xmlFile,outStr) |
| 385 |
nje01 |
1.2 |
|
| 386 |
nje01 |
1.1 |
if msLevel > 1: |
| 387 |
|
|
|
| 388 |
|
|
if not d.has_key('precursorMz') : |
| 389 |
|
|
print >>sys.stderr, "Required precursorMz attribute missing." |
| 390 |
|
|
sys.exit(1) |
| 391 |
|
|
|
| 392 |
|
|
# We scan the parent spectrum in the region of the |
| 393 |
|
|
# precursorMz to establish the intensity. Optionally, |
| 394 |
|
|
# we tune the precursorMz itself, on the basis of this |
| 395 |
|
|
|
| 396 |
|
|
pMz = d['precursorMz'] |
| 397 |
|
|
tol = self.reader.precursorPrecision(pMz) |
| 398 |
|
|
pMzLB = pMz-tol |
| 399 |
|
|
pMzUB = pMz+tol |
| 400 |
|
|
pMzIntensity = 0 |
| 401 |
|
|
|
| 402 |
|
|
if len(ancestors) > 0: |
| 403 |
|
|
for i in xrange(0,len(ancestors[-1][1]),2): |
| 404 |
|
|
x = ancestors[-1][1][i]; y = ancestors[-1][1][i+1]; |
| 405 |
|
|
if x < pMzLB: |
| 406 |
|
|
continue |
| 407 |
|
|
if x > pMzUB: |
| 408 |
|
|
break |
| 409 |
|
|
if pMzIntensity < y: |
| 410 |
|
|
pMzIntensity = y |
| 411 |
|
|
pMzTune = x |
| 412 |
|
|
|
| 413 |
|
|
if self.reader.precursorTune(): |
| 414 |
|
|
pMz = pMzTune |
| 415 |
|
|
|
| 416 |
|
|
outStr = "<precursorMz" |
| 417 |
|
|
for (k,v) in d.items(): |
| 418 |
|
|
if k.startswith('precursorMz.'): |
| 419 |
|
|
k,f = k.split(':') |
| 420 |
|
|
k = k[12:] |
| 421 |
|
|
outStr += (" %%s=\"%s\""%(f,))%(k,v) |
| 422 |
|
|
if len(ancestors)>0: |
| 423 |
|
|
outStr += " precursorScanNum=\"%d\""%(ancestors[-1][0],) |
| 424 |
|
|
outStr += " precursorIntensity=\"%f\">"%(pMzIntensity,) |
| 425 |
|
|
else: |
| 426 |
|
|
outStr += ">" |
| 427 |
|
|
outStr += "%f</precursorMz>\n" % (pMz,) |
| 428 |
|
|
self.writeString(xmlFile,outStr) |
| 429 |
|
|
|
| 430 |
nje01 |
1.3 |
if self.reader.maldi() and self.version in ('2.2',): |
| 431 |
nje01 |
1.1 |
outStr = '<maldi' |
| 432 |
|
|
for (k,v) in d.items(): |
| 433 |
|
|
if k.startswith('maldi.'): |
| 434 |
|
|
k,f = k.split(':') |
| 435 |
|
|
k = k[6:] |
| 436 |
|
|
outStr += (" %%s=\"%s\""%(f,))%(k,v) |
| 437 |
|
|
outStr += " plateID=\"%s\""%(d['plateID'],) |
| 438 |
|
|
outStr += " spotID=\"%s\""%(d['spotID'],) |
| 439 |
|
|
outStr += "/>\n" |
| 440 |
|
|
self.writeString(xmlFile,outStr) |
| 441 |
|
|
|
| 442 |
nje01 |
1.3 |
if sys.byteorder != 'big': |
| 443 |
|
|
s.byteswap() |
| 444 |
|
|
|
| 445 |
|
|
if debug: |
| 446 |
|
|
s = s[:20] |
| 447 |
|
|
|
| 448 |
|
|
specstr = s.tostring() |
| 449 |
|
|
if self.peakcompress: |
| 450 |
|
|
specstr = zlib.compress(specstr,9) |
| 451 |
|
|
outStr = "<peaks precision=\"32\" byteOrder=\"network\" contentType=\"m/z-int\" compressionType=\"zlib\" compressedLen=\"%d\">"%(len(specstr),) |
| 452 |
|
|
else: |
| 453 |
|
|
if float(self.version) >= 3.0: |
| 454 |
|
|
outStr = "<peaks precision=\"32\" byteOrder=\"network\" contentType=\"m/z-int\" compressionType=\"none\" compressedLen=\"%d\">"%(len(specstr),) |
| 455 |
|
|
else: |
| 456 |
|
|
outStr = "<peaks precision=\"32\" byteOrder=\"network\" pairOrder=\"m/z-int\">" |
| 457 |
|
|
|
| 458 |
nje01 |
1.1 |
self.writeString(xmlFile,outStr) |
| 459 |
|
|
|
| 460 |
|
|
# Spec says the byte order shall be |
| 461 |
|
|
# network, which is the same as big endian. |
| 462 |
|
|
|
| 463 |
|
|
if sys.byteorder != 'big': |
| 464 |
|
|
s.byteswap() |
| 465 |
|
|
|
| 466 |
nje01 |
1.3 |
outStr = b64encode(specstr) |
| 467 |
|
|
self.writeString(xmlFile,outStr) |
| 468 |
nje01 |
1.1 |
|
| 469 |
|
|
outStr = "</peaks>\n" |
| 470 |
|
|
self.writeString(xmlFile,outStr) |
| 471 |
|
|
|
| 472 |
nje01 |
1.3 |
if self.reader.maldi() and self.version not in ('2.2',): |
| 473 |
nje01 |
1.1 |
outStr = '' |
| 474 |
|
|
for (k,v) in d.items(): |
| 475 |
|
|
if k.startswith('maldi.'): |
| 476 |
|
|
k,f = k.split(':') |
| 477 |
|
|
k = k[6:] |
| 478 |
|
|
outStr += '<nameValue' |
| 479 |
nje01 |
1.3 |
outStr += ' name="maldi.%s"'%(k,) |
| 480 |
|
|
outStr += (' value="%s"'%(f,))%(v,) |
| 481 |
|
|
outStr += '/>\n' |
| 482 |
|
|
outStr += '<nameValue' |
| 483 |
|
|
outStr += ' name="maldi.plateID"' |
| 484 |
|
|
outStr += ' value="%s"'%(d['plateID'],) |
| 485 |
|
|
outStr += '/>\n' |
| 486 |
|
|
outStr += '<nameValue' |
| 487 |
|
|
outStr += ' name="maldi.spotID"' |
| 488 |
|
|
outStr += ' value="%s"'%(d['spotID'],) |
| 489 |
|
|
outStr += '/>\n' |
| 490 |
|
|
self.writeString(xmlFile,outStr) |
| 491 |
|
|
|
| 492 |
|
|
if self.version not in ('2.2',): |
| 493 |
|
|
outStr = '' |
| 494 |
|
|
for (k,v) in d.items(): |
| 495 |
|
|
if k.startswith('scanOrigin.'): |
| 496 |
|
|
k,f = k.split(':') |
| 497 |
|
|
k = k[11:] |
| 498 |
|
|
outStr += '<nameValue' |
| 499 |
|
|
outStr += ' name="scanOrigin.%s"'%(k,) |
| 500 |
|
|
outStr += (' value="%s"'%(f,))%(v,) |
| 501 |
nje01 |
1.1 |
outStr += '/>\n' |
| 502 |
nje01 |
1.3 |
self.writeString(xmlFile,outStr) |
| 503 |
|
|
|
| 504 |
|
|
outStr = '' |
| 505 |
|
|
for (k,v) in d.items(): |
| 506 |
|
|
if k.startswith('nameValue.'): |
| 507 |
|
|
k,f = k.split(':') |
| 508 |
|
|
k = k[10:] |
| 509 |
|
|
outStr += '<nameValue' |
| 510 |
|
|
outStr += ' name="%s"'%(k,) |
| 511 |
|
|
outStr += (' value="%s"'%(f,))%(v,) |
| 512 |
|
|
outStr += '/>\n' |
| 513 |
|
|
if len(outStr) > 0: |
| 514 |
nje01 |
1.1 |
self.writeString(xmlFile,outStr) |
| 515 |
|
|
|
| 516 |
|
|
xmlFile.flush() |
| 517 |
|
|
|
| 518 |
|
|
prevSpec = s |
| 519 |
|
|
|
| 520 |
|
|
outStr = "" |
| 521 |
nje01 |
1.4 |
for m in xrange(0,len(ancestors)+1): |
| 522 |
nje01 |
1.1 |
outStr += "</scan>\n" |
| 523 |
|
|
|
| 524 |
|
|
self.writeString(xmlFile,outStr) |
| 525 |
|
|
self.actualScanCount = scanNumber |
| 526 |
|
|
|
| 527 |
|
|
class ToMzData: |
| 528 |
|
|
def __init__(self,reader,filename,cmpfmt=None,filt=None): |
| 529 |
|
|
self.filename = filename |
| 530 |
|
|
self.compressfmt = cmpfmt |
| 531 |
|
|
self.reader = reader |
| 532 |
|
|
self.actualScanCount = 0 |
| 533 |
|
|
self.initSHA() |
| 534 |
|
|
self.filter = filt |
| 535 |
|
|
|
| 536 |
|
|
def writeString(self,fh,data): |
| 537 |
|
|
# self.writeByteCounter += len(data) |
| 538 |
|
|
self.sha1.update(data) |
| 539 |
|
|
fh.write(data) |
| 540 |
|
|
|
| 541 |
|
|
def initSHA(self): |
| 542 |
|
|
self.sha1 = sha.new() |
| 543 |
|
|
|
| 544 |
|
|
def updateSHA(self,s): |
| 545 |
|
|
self.sha1.update(s) |
| 546 |
|
|
|
| 547 |
|
|
def getSHA(self): |
| 548 |
|
|
return self.sha1.hexdigest().lower() |
| 549 |
|
|
|
| 550 |
|
|
def write(self,debug=False): |
| 551 |
|
|
|
| 552 |
|
|
# Make a temporary file for the scan data to count the number of spectra. |
| 553 |
|
|
(tmpFileFD,self.tmpFileName) = tempfile.mkstemp(dir='.',prefix='.pymsxml') |
| 554 |
|
|
tmpFile = os.fdopen(tmpFileFD,'wb') |
| 555 |
|
|
|
| 556 |
|
|
# Has a number of side effects, it fills in scanIndices, and sets self.actualScanCount. |
| 557 |
|
|
self.write_scans(tmpFile,debug) |
| 558 |
|
|
|
| 559 |
|
|
tmpFile.close() |
| 560 |
|
|
|
| 561 |
|
|
scanhash = self.getSHA() |
| 562 |
|
|
|
| 563 |
|
|
self.initSHA() |
| 564 |
|
|
|
| 565 |
|
|
if self.compressfmt == None and not self.filename.endswith('.gz'): |
| 566 |
|
|
xmlFile = open(self.filename,'wb') |
| 567 |
|
|
elif self.compressfmt == 'gz' or self.filename.endswith('.gz'): |
| 568 |
|
|
if self.filename.endswith('.gz'): |
| 569 |
|
|
xmlFile = gzip.open(self.filename,'wb') |
| 570 |
|
|
else: |
| 571 |
|
|
xmlFile = gzip.open(self.filename+'.gz','wb') |
| 572 |
|
|
else: |
| 573 |
|
|
print >>sys.stderr, "Bad compressfmt specification" |
| 574 |
|
|
sys.exit(1) |
| 575 |
|
|
|
| 576 |
|
|
self.writeString (xmlFile,'<?xml version="1.0" encoding="ISO-8859-1"?>\n') |
| 577 |
|
|
|
| 578 |
|
|
outStr = "<mzData " |
| 579 |
|
|
outStr += "version=\"1.05\" " |
| 580 |
|
|
outStr += "accessionNumber=\"pymsxml:%s\" "%(scanhash,) |
| 581 |
|
|
outStr += "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" " |
| 582 |
|
|
# outStr += "xmlns=\"http://psidev.sourceforge.net/ms/xml/mzdata\" " |
| 583 |
|
|
outStr += "xsi:noNamespaceSchemaLocation=\"http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.xsd\"" |
| 584 |
|
|
outStr += ">\n" |
| 585 |
|
|
|
| 586 |
|
|
self.writeString (xmlFile,outStr) |
| 587 |
|
|
|
| 588 |
|
|
outStr = "<description>\n" |
| 589 |
|
|
outStr += "<admin>\n" |
| 590 |
|
|
outStr += "<sampleName></sampleName>\n" |
| 591 |
|
|
outStr += "<contact>\n" |
| 592 |
|
|
outStr += "<name></name>\n" |
| 593 |
|
|
outStr += "<institution></institution>\n" |
| 594 |
|
|
outStr += "</contact>\n" |
| 595 |
|
|
outStr += "</admin>\n" |
| 596 |
|
|
outStr += "<instrument>\n" |
| 597 |
|
|
outStr += "<instrumentName></instrumentName>\n" |
| 598 |
|
|
outStr += "<source>\n" |
| 599 |
|
|
outStr += "</source>\n" |
| 600 |
|
|
outStr += "<analyzerList count=\"1\">\n" |
| 601 |
|
|
outStr += "<analyzer>\n" |
| 602 |
|
|
outStr += "</analyzer>\n" |
| 603 |
|
|
outStr += "</analyzerList>\n" |
| 604 |
|
|
outStr += "<detector>\n" |
| 605 |
|
|
outStr += "</detector>\n" |
| 606 |
|
|
outStr += "</instrument>\n" |
| 607 |
|
|
outStr += "<dataProcessing>\n" |
| 608 |
|
|
outStr += "<software>\n" |
| 609 |
|
|
outStr += "<name>%s</name>\n"%(self.reader.acquisitionSoftware(),) |
| 610 |
|
|
outStr += "<version>%s</version>\n"%(self.reader.acquisitionSoftwareVersion(),) |
| 611 |
|
|
outStr += "</software>\n" |
| 612 |
|
|
outStr += "<software>\n" |
| 613 |
|
|
nv = NameVersion() |
| 614 |
|
|
outStr += "<name>%s</name>\n"%(nv.name(),) |
| 615 |
|
|
outStr += "<version>%s</version>\n"%(nv.version(),) |
| 616 |
|
|
outStr += "</software>\n" |
| 617 |
|
|
outStr += "</dataProcessing>\n" |
| 618 |
|
|
outStr += "</description>\n" |
| 619 |
|
|
|
| 620 |
|
|
self.writeString (xmlFile,outStr) |
| 621 |
|
|
|
| 622 |
|
|
outStr = "<spectrumList" |
| 623 |
|
|
outStr += " count=\"%d\">\n"%(self.actualScanCount,) |
| 624 |
|
|
|
| 625 |
|
|
self.writeString (xmlFile,outStr) |
| 626 |
|
|
|
| 627 |
|
|
tmpFile = open(self.tmpFileName,'rb') |
| 628 |
|
|
while True: |
| 629 |
|
|
tmpStr = tmpFile.read(1024) |
| 630 |
|
|
if tmpStr == '': |
| 631 |
|
|
break |
| 632 |
|
|
self.writeString(xmlFile,tmpStr) |
| 633 |
|
|
tmpFile.close() |
| 634 |
|
|
os.unlink(self.tmpFileName) |
| 635 |
|
|
self.tmpFileName = '' |
| 636 |
|
|
|
| 637 |
|
|
outStr = "</spectrumList>\n</mzData>\n" |
| 638 |
|
|
|
| 639 |
|
|
self.writeString (xmlFile,outStr) |
| 640 |
|
|
|
| 641 |
|
|
def write_scans(self,xmlFile,debug=False): |
| 642 |
|
|
|
| 643 |
|
|
msLevel = 0 |
| 644 |
|
|
scanNumber = 0 |
| 645 |
|
|
ancestors = [] |
| 646 |
|
|
|
| 647 |
|
|
self.initSHA() |
| 648 |
|
|
# self.writeByteCounter = 0 |
| 649 |
|
|
|
| 650 |
|
|
for (s,d) in self.reader.spectra(): |
| 651 |
|
|
|
| 652 |
|
|
if self.filter != None and not self.filter.test(d): |
| 653 |
|
|
continue |
| 654 |
|
|
|
| 655 |
|
|
if debug and scanNumber >= 10: |
| 656 |
|
|
break |
| 657 |
|
|
|
| 658 |
|
|
if not d.has_key('msLevel'): |
| 659 |
|
|
print >>sys.stderr, "Required scan attributes missing." |
| 660 |
|
|
sys.exit(1) |
| 661 |
|
|
|
| 662 |
|
|
prevLevel = msLevel |
| 663 |
|
|
msLevel = d['msLevel'] |
| 664 |
|
|
|
| 665 |
|
|
if prevLevel < msLevel and prevLevel > 0: |
| 666 |
|
|
# We went "in" a level, push scan number of parent |
| 667 |
|
|
ancestors.append((scanNumber,prevSpec)) |
| 668 |
|
|
elif prevLevel > msLevel and msLevel > 0: |
| 669 |
|
|
ancestors.pop() |
| 670 |
|
|
|
| 671 |
|
|
scanNumber = scanNumber + 1 |
| 672 |
|
|
|
| 673 |
|
|
totIonCurrent = 0 |
| 674 |
|
|
maxmz = None |
| 675 |
|
|
minmz = None |
| 676 |
|
|
basePeakMz = None |
| 677 |
|
|
basePeakIntensity = None |
| 678 |
|
|
peaksCount = 0 |
| 679 |
|
|
for i in xrange(0,len(s),2): |
| 680 |
|
|
x = s[i]; y = s[i+1] |
| 681 |
|
|
if minmz is None or minmz > x: |
| 682 |
|
|
minmz = x |
| 683 |
|
|
if maxmz is None or maxmz < x: |
| 684 |
|
|
maxmz = x |
| 685 |
|
|
totIonCurrent += y |
| 686 |
|
|
if basePeakIntensity is None or basePeakIntensity < y: |
| 687 |
|
|
basePeakIntensity = y |
| 688 |
|
|
basePeakMz = x |
| 689 |
|
|
peaksCount += 1 |
| 690 |
|
|
|
| 691 |
|
|
outStr = "<spectrum id=\"%d\">\n" % (scanNumber,) |
| 692 |
|
|
outStr += "<spectrumDesc>\n" |
| 693 |
|
|
outStr += "<spectrumSettings>\n" |
| 694 |
|
|
|
| 695 |
|
|
self.writeString (xmlFile,outStr) |
| 696 |
|
|
|
| 697 |
|
|
# outStr += "<acqSpecification>\n" |
| 698 |
|
|
# outStr += "</acqSpecification>\n" |
| 699 |
|
|
|
| 700 |
|
|
outStr = "<spectrumInstrument" |
| 701 |
|
|
outStr += " msLevel=\"%d\""%(msLevel,) |
| 702 |
|
|
if d.has_key('scan.startMz') and \ |
| 703 |
|
|
d.has_key('scan.endMz'): |
| 704 |
|
|
outStr += " mzRangeStart=\"%f\""%(d['scan.startMz'],) |
| 705 |
|
|
outStr += " mzRangeStop=\"%f\""%(d['scan.endMz'],) |
| 706 |
|
|
outStr += ">\n" |
| 707 |
|
|
for (k,v) in d.items(): |
| 708 |
|
|
if k.startswith('scan.'): |
| 709 |
|
|
k,f = k.split(':') |
| 710 |
|
|
k = k[5:] |
| 711 |
|
|
|
| 712 |
|
|
if k == "polarity": |
| 713 |
|
|
if v == '+': |
| 714 |
|
|
outStr += "<cvParam cvLabel=\"\" accession=\"\" name=\"Polarity\" value=\"%s\"/>\n"%("Positive",) |
| 715 |
|
|
elif v == '-': |
| 716 |
|
|
outStr += "<cvParam cvLabel=\"\" accession=\"\" name=\"Polarity\" value=\"%s\"/>\n"%("Negative",) |
| 717 |
|
|
elif k == 'retentionTime': |
| 718 |
|
|
outStr += "<cvParam cvLabel=\"\" accession=\"\" name=\"TimeInSeconds\" value=\"%f\"/>\n"%(v,) |
| 719 |
|
|
else: |
| 720 |
|
|
outStr += ("<userParam name=\"%%s\" value=\"%s\"/>\n"%(f,))%(k,v) |
| 721 |
|
|
outStr += "<userParam name=\"lowMz\" value=\"%f\"/>\n"%(minmz,) |
| 722 |
|
|
outStr += "<userParam name=\"highMz\" value=\"%f\"/>\n"%(maxmz,) |
| 723 |
|
|
outStr += "<userParam name=\"totIonCurrent\" value=\"%f\"/>\n"%(totIonCurrent,) |
| 724 |
|
|
outStr += "<userParam name=\"basePeakMz\" value=\"%f\"/>\n"%(basePeakMz,) |
| 725 |
|
|
outStr += "<userParam name=\"basePeakIntensity\" value=\"%f\"/>\n"%(basePeakIntensity,) |
| 726 |
|
|
outStr += "</spectrumInstrument>\n" |
| 727 |
|
|
outStr += "</spectrumSettings>\n" |
| 728 |
|
|
|
| 729 |
|
|
self.writeString (xmlFile,outStr) |
| 730 |
|
|
|
| 731 |
|
|
if msLevel > 1: |
| 732 |
|
|
|
| 733 |
|
|
if not d.has_key('precursorMz') : |
| 734 |
|
|
print >>sys.stderr, "Required precursorMz attribute missing." |
| 735 |
|
|
sys.exit(1) |
| 736 |
|
|
|
| 737 |
|
|
# We scan the parent spectrum in the region of the |
| 738 |
|
|
# precursorMz to establish the intensity. Optionally, |
| 739 |
|
|
# we tune the precursorMz itself, on the basis of this |
| 740 |
|
|
|
| 741 |
|
|
pMz = d['precursorMz'] |
| 742 |
|
|
tol = self.reader.precursorPrecision(pMz) |
| 743 |
|
|
pMzLB = pMz-tol |
| 744 |
|
|
pMzUB = pMz+tol |
| 745 |
|
|
pMzIntensity = 0 |
| 746 |
|
|
|
| 747 |
|
|
for i in xrange(0,len(ancestors[-1][1]),2): |
| 748 |
|
|
x = ancestors[-1][1][i]; y = ancestors[-1][1][i+1]; |
| 749 |
|
|
if x < pMzLB: |
| 750 |
|
|
continue |
| 751 |
|
|
if x > pMzUB: |
| 752 |
|
|
break |
| 753 |
|
|
if pMzIntensity < y: |
| 754 |
|
|
pMzIntensity = y |
| 755 |
|
|
pMzTune = x |
| 756 |
|
|
|
| 757 |
|
|
if self.reader.precursorTune(): |
| 758 |
|
|
pMz = pMzTune |
| 759 |
|
|
|
| 760 |
|
|
outStr = "<precursorList count=\"1\">\n" |
| 761 |
|
|
|
| 762 |
|
|
outStr += "<precursor" |
| 763 |
|
|
outStr += " msLevel=\"%d\""%(msLevel,) |
| 764 |
|
|
outStr += " spectrumRef=\"%d\""%(ancestors[-1][0],) |
| 765 |
|
|
outStr += ">\n" |
| 766 |
|
|
|
| 767 |
|
|
self.writeString(xmlFile,outStr) |
| 768 |
|
|
|
| 769 |
|
|
outStr = "<ionSelection>\n" |
| 770 |
|
|
outStr += "<cvParam cvLabel=\"\" accession=\"\" name=\"MassToChargeRatio\" value=\"%f\"/>\n"%(pMz,) |
| 771 |
|
|
outStr += "<cvParam cvLabel=\"\" accession=\"\" name=\"Intensity\" value=\"%f\"/>\n"%(pMzIntensity,) |
| 772 |
|
|
for (k,v) in d.items(): |
| 773 |
|
|
if k.startswith('precursorMz.'): |
| 774 |
|
|
k,f = k.split(':') |
| 775 |
|
|
k = k[12:] |
| 776 |
|
|
outStr += ("<userParam name=\"%%s\" value=\"%s\"/>\n"%(f,))%(k,v) |
| 777 |
|
|
outStr += "</ionSelection>\n" |
| 778 |
|
|
|
| 779 |
|
|
self.writeString(xmlFile,outStr) |
| 780 |
|
|
|
| 781 |
|
|
outStr = "<activation>\n" |
| 782 |
|
|
outStr += "</activation>\n" |
| 783 |
|
|
outStr += "</precursor>\n" |
| 784 |
|
|
outStr += "</precursorList>\n" |
| 785 |
|
|
|
| 786 |
|
|
self.writeString(xmlFile,outStr) |
| 787 |
|
|
|
| 788 |
|
|
if self.reader.maldi(): |
| 789 |
|
|
outStr = '<maldi' |
| 790 |
|
|
for (k,v) in d.items(): |
| 791 |
|
|
if k.startswith('maldi.'): |
| 792 |
|
|
k,f = k.split(':') |
| 793 |
|
|
k = k[6:] |
| 794 |
|
|
outStr += (" %%s=\"%s\""%(f,))%(k,v) |
| 795 |
|
|
outStr += " plateID=\"%s\""%(d['plateID'],) |
| 796 |
|
|
outStr += " spotID=\"%s\""%(d['spotID'],) |
| 797 |
|
|
outStr += "/>\n" |
| 798 |
|
|
self.writeString(xmlFile,outStr) |
| 799 |
|
|
|
| 800 |
|
|
outStr = "</spectrumDesc>\n" |
| 801 |
|
|
self.writeString(xmlFile,outStr) |
| 802 |
|
|
|
| 803 |
|
|
outStr = "<mzArrayBinary>\n" |
| 804 |
|
|
outStr += "<data" |
| 805 |
|
|
outStr += " precision=\"32\"" |
| 806 |
|
|
outStr += " endian=\"%s\""%(sys.byteorder,) |
| 807 |
|
|
outStr += " length=\"%d\""%(peaksCount,) |
| 808 |
|
|
outStr += ">" |
| 809 |
|
|
self.writeString(xmlFile,outStr) |
| 810 |
|
|
|
| 811 |
|
|
outStr = b64encode(s[0:peaksCount*2:2].tostring()) |
| 812 |
|
|
if not debug: |
| 813 |
|
|
self.writeString(xmlFile,outStr) |
| 814 |
|
|
else: |
| 815 |
|
|
self.writeString(xmlFile,outStr[0:100]) |
| 816 |
|
|
|
| 817 |
|
|
outStr = "</data>\n</mzArrayBinary>\n" |
| 818 |
|
|
self.writeString(xmlFile,outStr) |
| 819 |
|
|
|
| 820 |
|
|
outStr = "<intenArrayBinary>\n" |
| 821 |
|
|
outStr += "<data" |
| 822 |
|
|
outStr += " precision=\"32\"" |
| 823 |
|
|
outStr += " endian=\"%s\""%(sys.byteorder,) |
| 824 |
|
|
outStr += " length=\"%d\""%(peaksCount,) |
| 825 |
|
|
outStr += ">" |
| 826 |
|
|
self.writeString(xmlFile,outStr) |
| 827 |
|
|
|
| 828 |
|
|
outStr = b64encode(s[1:peaksCount*2:2].tostring()) |
| 829 |
|
|
if not debug: |
| 830 |
|
|
self.writeString(xmlFile,outStr) |
| 831 |
|
|
else: |
| 832 |
|
|
self.writeString(xmlFile,outStr[0:100]) |
| 833 |
|
|
|
| 834 |
|
|
outStr = "</data>\n</intenArrayBinary>\n" |
| 835 |
|
|
self.writeString(xmlFile,outStr) |
| 836 |
|
|
|
| 837 |
|
|
if self.reader.maldi(): |
| 838 |
|
|
outStr = '' |
| 839 |
|
|
for (k,v) in d.items(): |
| 840 |
|
|
if k.startswith('maldi.'): |
| 841 |
|
|
k,f = k.split(':') |
| 842 |
|
|
k = k[6:] |
| 843 |
|
|
outStr += '<nameValue' |
| 844 |
|
|
outStr += ' name="%s"'%(k,) |
| 845 |
|
|
outStr += (' value="%f"'%(f,))%(v,) |
| 846 |
|
|
outStr += '/>\n' |
| 847 |
|
|
## outStr += '<nameValue' |
| 848 |
|
|
## outStr += ' name="plateID"' |
| 849 |
|
|
## outStr += ' value="%s"'%(d['plateID'],) |
| 850 |
|
|
## outStr += '/>\n' |
| 851 |
|
|
## outStr += '<nameValue' |
| 852 |
|
|
## outStr += ' name="spotID"' |
| 853 |
|
|
## outStr += ' value="%s"'%(d['spotID'],) |
| 854 |
|
|
## outStr += '/>\n' |
| 855 |
|
|
self.writeString(xmlFile,outStr) |
| 856 |
|
|
|
| 857 |
|
|
outStr = "</spectrum>\n" |
| 858 |
|
|
self.writeString(xmlFile,outStr) |
| 859 |
|
|
xmlFile.flush() |
| 860 |
|
|
|
| 861 |
|
|
prevSpec = s |
| 862 |
|
|
|
| 863 |
|
|
self.actualScanCount = scanNumber |
| 864 |
|
|
|
| 865 |
|
|
class QStarWiff: |
| 866 |
|
|
def __init__(self,filename,peaks=None): |
| 867 |
|
|
self.filename = filename |
| 868 |
|
|
self.filehash = fileSHA(filename) |
| 869 |
|
|
self.theTIC = None |
| 870 |
|
|
self.theWF = None |
| 871 |
|
|
self.theFMANSpecData = None |
| 872 |
|
|
self.startTime = None |
| 873 |
|
|
self.stopTime = None |
| 874 |
nje01 |
1.2 |
self.applyPeakDetect = [] |
| 875 |
nje01 |
1.1 |
if peaks: |
| 876 |
|
|
self.applyPeakDetect = map(int,peaks.split(',')) |
| 877 |
|
|
|
| 878 |
|
|
if not os.path.exists(self.filename): |
| 879 |
|
|
print >>sys.stderr, "Filename %s does not exist."%(self.filename,) |
| 880 |
|
|
sys.exit(1) |
| 881 |
|
|
|
| 882 |
|
|
self.filename = os.path.abspath(self.filename) |
| 883 |
|
|
|
| 884 |
|
|
def __del__(self): |
| 885 |
|
|
# Probably unnecessary |
| 886 |
|
|
self.close() |
| 887 |
|
|
|
| 888 |
|
|
def peakDetect(self,msLevel): |
| 889 |
|
|
return ((msLevel in self.applyPeakDetect) and (msLevel != 1)) |
| 890 |
|
|
|
| 891 |
|
|
def open(self): |
| 892 |
|
|
|
| 893 |
|
|
if self.theTIC is None: |
| 894 |
|
|
|
| 895 |
|
|
from win32com.client import Dispatch |
| 896 |
|
|
|
| 897 |
|
|
self.theFMANSpecData = Dispatch('Analyst.FMANSpecData') |
| 898 |
|
|
self.theTIC = Dispatch('Analyst.FMANChromData') |
| 899 |
|
|
self.theSPL = Dispatch('Analyst.SpectralPeakList') |
| 900 |
|
|
|
| 901 |
|
|
self.theFMANSpecData.WiffFileName = self.filename |
| 902 |
|
|
self.theTIC.WiffFileName = self.filename |
| 903 |
|
|
self.theWF = self.theFMANSpecData.GetWiffFileObject() |
| 904 |
|
|
|
| 905 |
|
|
self.theTIC.SetToTIC(1,0,0) |
| 906 |
|
|
|
| 907 |
|
|
self.startTime = self.theTIC.GetDataPointXValue(1) |
| 908 |
|
|
self.stopTime = self.theTIC.GetDataPointXValue(self.theTIC.GetNumberOfDataPoints()) |
| 909 |
|
|
|
| 910 |
|
|
def close(self): |
| 911 |
|
|
|
| 912 |
|
|
if not self.theTIC is None: |
| 913 |
|
|
|
| 914 |
|
|
if not self.theWF is None: |
| 915 |
|
|
self.theWF.CloseWiffFile() |
| 916 |
|
|
self.theTIC = None |
| 917 |
|
|
self.theFMANSpecData = None |
| 918 |
|
|
self.theWF = None |
| 919 |
|
|
|
| 920 |
|
|
def spectra(self): |
| 921 |
|
|
self.open() |
| 922 |
|
|
spectrumCount=0; |
| 923 |
|
|
|
| 924 |
|
|
numberOfSamples = self.theWF.GetActualNumberOfSamples() |
| 925 |
|
|
for i in xrange(1,numberOfSamples+1): |
| 926 |
|
|
|
| 927 |
|
|
# print >>sys.stderr, "Sample %d"%i |
| 928 |
|
|
# print >>sys.stderr, "Sample Name: %s"%(self.theWF.GetSampleName(i),) |
| 929 |
|
|
|
| 930 |
|
|
sampleName = self.theWF.GetSampleName(i) |
| 931 |
|
|
|
| 932 |
|
|
numberOfPeriods = self.theWF.GetActualNumberOfPeriods(i) |
| 933 |
|
|
for j in xrange(0,numberOfPeriods): |
| 934 |
|
|
|
| 935 |
|
|
numberOfExperiments = self.theWF.GetNumberOfExperiments(i,j) |
| 936 |
|
|
self.theTIC.SetToTIC(i, j, 0) |
| 937 |
|
|
|
| 938 |
|
|
numberOfTICDataPoints = self.theTIC.GetNumberOfDataPoints() |
| 939 |
|
|
for l in xrange(1,numberOfTICDataPoints+1): |
| 940 |
|
|
|
| 941 |
|
|
for k in xrange(0,numberOfExperiments): |
| 942 |
|
|
|
| 943 |
|
|
self.theExperiment = self.theWF.GetExperimentObject(i, j, k) |
| 944 |
|
|
self.theTIC.SetToTIC(i, j, k) |
| 945 |
|
|
|
| 946 |
|
|
# Convert to seconds? |
| 947 |
|
|
xValue = self.theTIC.GetDataPointXValue(l) * 60 |
| 948 |
|
|
|
| 949 |
|
|
spectrumCount += 1; |
| 950 |
|
|
|
| 951 |
|
|
# If any Ion current at time "l" |
| 952 |
|
|
if self.theTIC.GetDataPointYValue(l) > 0: |
| 953 |
|
|
|
| 954 |
|
|
self.theFMANSpecData.SetSpectrum(i, j, k, xValue, xValue) |
| 955 |
|
|
|
| 956 |
|
|
if self.theExperiment.ScanType == 9: |
| 957 |
|
|
msLevel = 2 |
| 958 |
|
|
m = re.search(r'[(]([0-9.]+)[)]',self.theFMANSpecData.DataTitle) |
| 959 |
|
|
fixedMass = float(m.group(1)) |
| 960 |
|
|
else: |
| 961 |
|
|
msLevel = 1 |
| 962 |
|
|
|
| 963 |
|
|
startMass = self.theFMANSpecData.GetStartMass() |
| 964 |
|
|
stopMass = self.theFMANSpecData.GetStopMass() |
| 965 |
|
|
dataArr = array('f'); |
| 966 |
|
|
peakDetect = 'False' |
| 967 |
|
|
if self.peakDetect(msLevel): |
| 968 |
|
|
peakDetect = 'True' |
| 969 |
|
|
minY,maxY = self.theFMANSpecData.GetYValueRange() |
| 970 |
nje01 |
1.3 |
# print minY,maxY |
| 971 |
nje01 |
1.1 |
self.theFMANSpecData.Threshold(maxY*0.01) |
| 972 |
|
|
self.theSPL.FindPeaksInDataObject(self.theFMANSpecData,50.0) |
| 973 |
|
|
numPeaks = self.theSPL.GetNumberOfPeaks() |
| 974 |
nje01 |
1.3 |
# print numPeaks |
| 975 |
nje01 |
1.1 |
for m in xrange(1,numPeaks+1): |
| 976 |
|
|
(x,w,y,yp) = self.theSPL.GetPeak(m) |
| 977 |
|
|
if y <= 0: |
| 978 |
|
|
continue |
| 979 |
|
|
dataArr.append(x) |
| 980 |
|
|
dataArr.append(y) |
| 981 |
|
|
else: |
| 982 |
|
|
numPoints = self.theFMANSpecData.GetNumberOfDataPoints() |
| 983 |
|
|
for m in xrange(1,numPoints+1): |
| 984 |
|
|
if self.theFMANSpecData.GetDataPointYValue(m) <= 0: |
| 985 |
|
|
continue |
| 986 |
|
|
x = self.theFMANSpecData.GetDataPointXValue(m) |
| 987 |
|
|
dataArr.append(x) |
| 988 |
|
|
y = self.theFMANSpecData.GetDataPointYValue(m) |
| 989 |
|
|
dataArr.append(y) |
| 990 |
|
|
polarity = self.theExperiment.Polarity |
| 991 |
|
|
|
| 992 |
|
|
if len(dataArr) == 0: |
| 993 |
|
|
continue |
| 994 |
|
|
|
| 995 |
|
|
if polarity == 0: |
| 996 |
|
|
polarity_val = "+" |
| 997 |
|
|
else: |
| 998 |
|
|
polarity_val = "-" |
| 999 |
|
|
|
| 1000 |
|
|
rt = "PT%fS"%(xValue,) |
| 1001 |
|
|
|
| 1002 |
|
|
# Scan level attributes |
| 1003 |
|
|
# Required by mzXML (no format spec. needed) |
| 1004 |
nje01 |
1.3 |
d = {'msLevel':msLevel} |
| 1005 |
nje01 |
1.1 |
# Optional ('scan.' and prefixformat spec. needed) |
| 1006 |
|
|
d.update({ |
| 1007 |
|
|
'scan.retentionTime:PT%fS':xValue, |
| 1008 |
|
|
'scan.polarity:%s':polarity_val, |
| 1009 |
|
|
'scan.startMz:%f':startMass, |
| 1010 |
|
|
'scan.endMz:%f':stopMass, |
| 1011 |
|
|
}) |
| 1012 |
nje01 |
1.2 |
d.update({'scanOrigin.parentFileID:%s': self.filehash, |
| 1013 |
nje01 |
1.1 |
'scanOrigin.num:%d': spectrumCount}) |
| 1014 |
nje01 |
1.3 |
d.update({'nameValue.sample:%d':i, |
| 1015 |
|
|
'nameValue.period:%d':j, |
| 1016 |
|
|
'nameValue.experiment:%d':k, |
| 1017 |
|
|
'nameValue.sampleName:%s':sampleName}) |
| 1018 |
|
|
|
| 1019 |
nje01 |
1.1 |
if msLevel == 1: |
| 1020 |
|
|
yield (dataArr,d) |
| 1021 |
|
|
else: |
| 1022 |
|
|
# tandem MS scans add the following |
| 1023 |
|
|
# Required by mzXML |
| 1024 |
|
|
d.update({'precursorMz':fixedMass}) |
| 1025 |
|
|
# Optional |
| 1026 |
|
|
# d.update({'precursorMz.precursorMzIntensity:f':0.0}) |
| 1027 |
|
|
yield (dataArr,d) |
| 1028 |
|
|
|
| 1029 |
|
|
def getMsRunMetaData(self): |
| 1030 |
|
|
self.open() |
| 1031 |
|
|
d = {'startTime:PT%fS':self.startTime, |
| 1032 |
|
|
'endTime:PT%fS':self.stopTime, |
| 1033 |
|
|
} |
| 1034 |
|
|
return d |
| 1035 |
|
|
|
| 1036 |
|
|
def getFilenames(self): |
| 1037 |
|
|
return [ (self.filename,self.filehash) ] |
| 1038 |
|
|
|
| 1039 |
nje01 |
1.3 |
def msInstrumentID(self): |
| 1040 |
|
|
return "1" |
| 1041 |
|
|
|
| 1042 |
nje01 |
1.1 |
def msManufacturer(self): |
| 1043 |
|
|
return "ABI / SCIEX" |
| 1044 |
|
|
|
| 1045 |
|
|
def msModel(self): |
| 1046 |
|
|
return "QSTAR" |
| 1047 |
|
|
|
| 1048 |
|
|
def msIonisation(self): |
| 1049 |
|
|
return "ESI" |
| 1050 |
|
|
|
| 1051 |
|
|
def msMassAnalyzer(self): |
| 1052 |
|
|
return "Quadrupole" |
| 1053 |
|
|
|
| 1054 |
|
|
def msDetector(self): |
| 1055 |
nje01 |
1.3 |
return "LE" |
| 1056 |
nje01 |
1.1 |
|
| 1057 |
|
|
def acquisitionSoftware(self): |
| 1058 |
|
|
return "Analyst" |
| 1059 |
|
|
|
| 1060 |
|
|
def acquisitionSoftwareVersion(self): |
| 1061 |
|
|
return "1.0" |
| 1062 |
|
|
|
| 1063 |
|
|
def precursorPrecision(self,mz): |
| 1064 |
|
|
return .1 |
| 1065 |
|
|
|
| 1066 |
|
|
def precursorTune(self): |
| 1067 |
|
|
return True |
| 1068 |
|
|
|
| 1069 |
|
|
def lc(self): |
| 1070 |
|
|
return True |
| 1071 |
|
|
|
| 1072 |
|
|
def maldi(self): |
| 1073 |
|
|
return not self.lc() |
| 1074 |
|
|
|
| 1075 |
|
|
class mzXML_md_sax(handler.ContentHandler): |
| 1076 |
|
|
|
| 1077 |
|
|
def __init__(self): |
| 1078 |
|
|
self.md = {} |
| 1079 |
|
|
self.context = '' |
| 1080 |
|
|
|
| 1081 |
|
|
def startElement(self, name, attrs): |
| 1082 |
|
|
self.context += ':%s'%(name,) |
| 1083 |
|
|
# print >>sys.stderr, ">>",self.context |
| 1084 |
|
|
# sys.stderr.flush() |
| 1085 |
|
|
if self.context.endswith(':msRun'): |
| 1086 |
nje01 |
1.4 |
if attrs.has_key('startTime'): |
| 1087 |
|
|
self.md['startTime'] = float(attrs['startTime'][2:-1]) |
| 1088 |
|
|
if attrs.has_key('endTime'): |
| 1089 |
|
|
self.md['endTime'] = float(attrs['endTime'][2:-1]) |
| 1090 |
nje01 |
1.1 |
elif self.context.endswith(':parentFile'): |
| 1091 |
nje01 |
1.4 |
if not self.md.has_key('parentFile'): |
| 1092 |
|
|
self.md['parentFile'] = [] |
| 1093 |
|
|
self.md['parentFile'].append((unquote(attrs['fileName']),attrs['fileType'],attrs['fileSha1'])) |
| 1094 |
nje01 |
1.1 |
elif self.context.endswith(':instrument'): |
| 1095 |
|
|
self.md['msManufacturer'] = attrs['manufacturer'] |
| 1096 |
|
|
self.md['msModel'] = attrs['model'] |
| 1097 |
|
|
self.md['msIonisation'] = attrs['ionisation'] |
| 1098 |
|
|
self.md['msMassAnalyzer'] = attrs['msType'] |
| 1099 |
|
|
elif self.context.endswith(':msInstrument:msManufacturer'): |
| 1100 |
|
|
self.md['msManufacturer'] = attrs['value'] |
| 1101 |
|
|
elif self.context.endswith(':msInstrument:msModel'): |
| 1102 |
|
|
self.md['msModel'] = attrs['value'] |
| 1103 |
|
|
elif self.context.endswith(':msInstrument:msIonisation'): |
| 1104 |
|
|
self.md['msIonisation'] = attrs['value'] |
| 1105 |
|
|
elif self.context.endswith(':msInstrument:msMassAnalyzer'): |
| 1106 |
|
|
self.md['msMassAnalyzer'] = attrs['value'] |
| 1107 |
|
|
elif self.context.endswith(':msInstrument:msDetector'): |
| 1108 |
|
|
self.md['msDetector'] = attrs['value'] |
| 1109 |
|
|
elif self.context.endswith(':msInstrument:software'): |
| 1110 |
|
|
if attrs['type'] == 'acquisition': |
| 1111 |
|
|
self.md['acquisitionSoftware'] = attrs['name'] |
| 1112 |
|
|
self.md['acquisitionSoftwareVersion'] = attrs['version'] |
| 1113 |
|
|
elif self.context.endswith(':instrument:software'): |
| 1114 |
|
|
if attrs['type'] == 'acquisition': |
| 1115 |
|
|
self.md['acquisitionSoftware'] = attrs['name'] |
| 1116 |
|
|
self.md['acquisitionSoftwareVersion'] = attrs['version'] |
| 1117 |
|
|
elif self.context.endswith(':scan'): |
| 1118 |
|
|
raise SAXException("Early termination") |
| 1119 |
|
|
|
| 1120 |
|
|
def endElement(self, name): |
| 1121 |
|
|
# print >>sys.stderr, "<<",self.context |
| 1122 |
|
|
# sys.stderr.flush() |
| 1123 |
|
|
self.context = self.context[0:-(len(name)+1)] |
| 1124 |
|
|
|
| 1125 |
|
|
|
| 1126 |
|
|
class mzXML_spec_sax(handler.ContentHandler): |
| 1127 |
|
|
|
| 1128 |
|
|
def __init__(self): |
| 1129 |
|
|
self.context = '' |
| 1130 |
|
|
self.content = '' |
| 1131 |
|
|
self.spectra = [] |
| 1132 |
|
|
self.done = False |
| 1133 |
|
|
self.scancount = 0 |
| 1134 |
|
|
self.scanmax = 1000 |
| 1135 |
|
|
self.scanstart = 0 |
| 1136 |
|
|
|
| 1137 |
|
|
def startElement(self, name, attrs): |
| 1138 |
|
|
self.context += ':%s'%(name,) |
| 1139 |
|
|
# print >>sys.stderr, ">>",self.context |
| 1140 |
|
|
# sys.stderr.flush() |
| 1141 |
|
|
self.content = '' |
| 1142 |
|
|
if name == 'scan': |
| 1143 |
|
|
self.scanmd = {} |
| 1144 |
|
|
self.scanlevel = int(attrs['msLevel']) |
| 1145 |
|
|
self.scannum = int(attrs['num']) |
| 1146 |
|
|
if attrs.has_key('retentionTime'): |
| 1147 |
|
|
self.rt = float(attrs['retentionTime'][2:-1]) |
| 1148 |
nje01 |
1.4 |
if attrs.has_key('endMz'): |
| 1149 |
|
|
self.endMz = float(attrs['endMz']) |
| 1150 |
|
|
if attrs.has_key('startMz'): |
| 1151 |
|
|
self.startMz = float(attrs['startMz']) |
| 1152 |
nje01 |
1.1 |
self.polarity = attrs.get('polarity',None) |
| 1153 |
|
|
for (k,v) in attrs.items(): |
| 1154 |
|
|
self.scanmd[k] = v |
| 1155 |
|
|
self.precursorMz = None |
| 1156 |
|
|
self.scancount += 1 |
| 1157 |
|
|
elif name == 'msRun': |
| 1158 |
|
|
self.scancount = 0 |
| 1159 |
|
|
self.spectra = [] |
| 1160 |
|
|
self.context = ':msRun' |
| 1161 |
|
|
elif name == 'scanOrigin': |
| 1162 |
|
|
self.scanmd['scanOrigin'] = attrs |
| 1163 |
nje01 |
1.5 |
elif self.context.endswith(':scan:nameValue'): |
| 1164 |
|
|
self.scanmd['nameValue.%s:%%s'%attrs['name']] = attrs['value'] |
| 1165 |
nje01 |
1.1 |
|
| 1166 |
|
|
def characters(self, content): |
| 1167 |
|
|
if self.scancount >= self.scanstart: |
| 1168 |
|
|
if self.context.endswith(':peaks') or \ |
| 1169 |
|
|
self.context.endswith(':precursorMz'): |
| 1170 |
|
|
self.content += content |
| 1171 |
|
|
|
| 1172 |
|
|
def endElement(self, name): |
| 1173 |
|
|
if self.scancount >= self.scanstart: |
| 1174 |
|
|
if self.context.endswith('scan:peaks'): |
| 1175 |
|
|
|
| 1176 |
nje01 |
1.5 |
self.spec = array('f') |
| 1177 |
nje01 |
1.1 |
# print >>sys.stderr, len(self.content), len(b64decode(self.content)), self.content |
| 1178 |
nje01 |
1.5 |
self.spec.fromstring(b64decode(self.content)) |
| 1179 |
nje01 |
1.1 |
if sys.byteorder != 'big': |
| 1180 |
nje01 |
1.5 |
self.spec.byteswap() |
| 1181 |
|
|
elif self.context.endswith(':scan'): |
| 1182 |
nje01 |
1.1 |
d = {'msLevel':self.scanlevel} |
| 1183 |
|
|
# Optional ('scan.' and prefixformat spec. needed) |
| 1184 |
nje01 |
1.4 |
if hasattr(self,'rt'): |
| 1185 |
|
|
d.update({'scan.retentionTime:PT%fS':self.rt}) |
| 1186 |
|
|
if hasattr(self,'startMz'): |
| 1187 |
|
|
d.update({'scan.startMz:%f':self.startMz}) |
| 1188 |
|
|
if hasattr(self,'endMz'): |
| 1189 |
|
|
d.update({'scan.endMz:%f':self.endMz}) |
| 1190 |
nje01 |
1.1 |
if self.polarity != None: |
| 1191 |
|
|
d.update({'scan.polarity:%s':self.polarity}) |
| 1192 |
|
|
if self.scanlevel == 2: |
| 1193 |
|
|
d.update({'precursorMz':self.precursorMz}) |
| 1194 |
|
|
if self.scanmd.has_key('scanOrigin'): |
| 1195 |
nje01 |
1.2 |
d.update({'scanOrigin.parentFileID:%s': self.scanmd['scanOrigin']['parentFileID'], |
| 1196 |
nje01 |
1.5 |
'scanOrigin.num:%d': int(self.scanmd['scanOrigin']['num'])}) |
| 1197 |
nje01 |
1.1 |
for (k,v) in self.scanmd.items(): |
| 1198 |
|
|
if not d.has_key(k): |
| 1199 |
|
|
d[k] = v |
| 1200 |
nje01 |
1.5 |
self.spectra.append((self.spec,d)) |
| 1201 |
nje01 |
1.1 |
if len(self.spectra) >= self.scanmax: |
| 1202 |
|
|
self.scanstart = self.scancount+1 |
| 1203 |
|
|
raise SAXException("Early termination") |
| 1204 |
|
|
elif self.context.endswith('scan:precursorMz'): |
| 1205 |
|
|
self.precursorMz = float(self.content) |
| 1206 |
|
|
if self.context.endswith('msRun'): |
| 1207 |
|
|
self.done = True |
| 1208 |
|
|
# print >>sys.stderr, "<<",self.context |
| 1209 |
|
|
# sys.stderr.flush() |
| 1210 |
|
|
self.context = self.context[0:-(len(name)+1)] |
| 1211 |
|
|
|
| 1212 |
|
|
class FromMzXML: |
| 1213 |
|
|
def __init__(self,filename): |
| 1214 |
|
|
self.filename = filename |
| 1215 |
|
|
self.parser = None |
| 1216 |
|
|
|
| 1217 |
|
|
if not os.path.exists(self.filename): |
| 1218 |
|
|
print >>sys.stderr, "Filename %s does not exist."%(self.filename,) |
| 1219 |
|
|
sys.exit(1) |
| 1220 |
|
|
|
| 1221 |
|
|
if self.filename.endswith('.gz'): |
| 1222 |
|
|
self.compressfmt = 'gz' |
| 1223 |
|
|
else: |
| 1224 |
|
|
self.compressfmt = None |
| 1225 |
|
|
|
| 1226 |
|
|
def __del__(self): |
| 1227 |
|
|
self.close() |
| 1228 |
|
|
|
| 1229 |
|
|
def open(self): |
| 1230 |
|
|
|
| 1231 |
|
|
if self.parser == None: |
| 1232 |
|
|
# print >>sys.stderr, "Parsing out meta-data..." |
| 1233 |
|
|
# sys.stderr.flush() |
| 1234 |
|
|
self.parser = make_parser() |
| 1235 |
|
|
self.handler = mzXML_md_sax() |
| 1236 |
|
|
self.parser.setContentHandler(self.handler) |
| 1237 |
|
|
try: |
| 1238 |
|
|
if self.compressfmt == None: |
| 1239 |
|
|
self.parser.parse(self.filename) |
| 1240 |
|
|
elif self.compressfmt == 'gz': |
| 1241 |
|
|
self.parser.parse(gzip.open(self.filename,'r')) |
| 1242 |
|
|
else: |
| 1243 |
|
|
print >>sys.stderr, "Bad compressfmt specification: %s"%(self.compressfmt,) |
| 1244 |
|
|
sys.exit(1) |
| 1245 |
|
|
except SAXException: |
| 1246 |
|
|
pass |
| 1247 |
|
|
|
| 1248 |
|
|
self.md = self.handler.md |
| 1249 |
|
|
|
| 1250 |
|
|
# print >>sys.stderr, self.md |
| 1251 |
|
|
# sys.stderr.flush() |
| 1252 |
|
|
|
| 1253 |
|
|
# print >>sys.stderr, "Set up spectrum parser..." |
| 1254 |
|
|
# sys.stderr.flush() |
| 1255 |
|
|
self.parser = make_parser() |
| 1256 |
|
|
self.handler = mzXML_spec_sax() |
| 1257 |
|
|
self.parser.setContentHandler(self.handler) |
| 1258 |
|
|
|
| 1259 |
|
|
def close(self): |
| 1260 |
|
|
pass |
| 1261 |
|
|
|
| 1262 |
|
|
def spectra(self): |
| 1263 |
|
|
self.open() |
| 1264 |
|
|
while True: |
| 1265 |
|
|
# print >>sys.stderr, "Spectrum parser to read spectra from",self.handler.scanstart |
| 1266 |
|
|
# sys.stderr.flush() |
| 1267 |
|
|
try: |
| 1268 |
|
|
if self.compressfmt == None: |
| 1269 |
|
|
self.parser.parse(self.filename) |
| 1270 |
|
|
elif self.compressfmt == 'gz': |
| 1271 |
|
|
self.parser.parse(gzip.open(self.filename,'r')) |
| 1272 |
|
|
else: |
| 1273 |
|
|
print >>sys.stderr, "Bad compressfmt specification: %s"%(self.compressfmt,) |
| 1274 |
|
|
sys.exit(1) |
| 1275 |
|
|
except SAXException: |
| 1276 |
|
|
pass |
| 1277 |
|
|
for (s,d) in self.handler.spectra: |
| 1278 |
|
|
# print >>sys.stderr, "Yeild spectrum number:",d['num'] |
| 1279 |
|
|
yield (s,d) |
| 1280 |
|
|
if self.handler.done: |
| 1281 |
|
|
break |
| 1282 |
|
|
|
| 1283 |
|
|
def getMsRunMetaData(self): |
| 1284 |
|
|
self.open() |
| 1285 |
nje01 |
1.4 |
d = {} |
| 1286 |
|
|
if self.md.has_key('startTime'): |
| 1287 |
|
|
d.update({'startTime:PT%fS':self.md['startTime']}) |
| 1288 |
|
|
if self.md.has_key('endTime'): |
| 1289 |
|
|
d.update({'endTime:PT%fS':self.md['endTime']}) |
| 1290 |
nje01 |
1.1 |
return d |
| 1291 |
|
|
|
| 1292 |
|
|
def getFilenames(self): |
| 1293 |
nje01 |
1.4 |
return self.md['parentFile'] |
| 1294 |
|
|
|
| 1295 |
|
|
def msInstrumentID(self): |
| 1296 |
|
|
return "1" |
| 1297 |
|
|
|
| 1298 |
|
|
def peakDetect(self,level): |
| 1299 |
|
|
return False |
| 1300 |
nje01 |
1.1 |
|
| 1301 |
|
|
def msManufacturer(self): |
| 1302 |
|
|
return self.md.get('msManufacturer','') |
| 1303 |
|
|
|
| 1304 |
|
|
def msModel(self): |
| 1305 |
|
|
return self.md.get('msModel','') |
| 1306 |
|
|
|
| 1307 |
|
|
def msIonisation(self): |
| 1308 |
|
|
return self.md.get('msIonisation','') |
| 1309 |
|
|
|
| 1310 |
|
|
def msMassAnalyzer(self): |
| 1311 |
|
|
return self.md.get('msMassAnalyzer','') |
| 1312 |
|
|
|
| 1313 |
|
|
def msDetector(self): |
| 1314 |
|
|
return self.md.get('msDetector','') |
| 1315 |
|
|
|
| 1316 |
|
|
def acquisitionSoftware(self): |
| 1317 |
|
|
return self.md.get('acquisitionSoftware','') |
| 1318 |
|
|
|
| 1319 |
|
|
def acquisitionSoftwareVersion(self): |
| 1320 |
|
|
return self.md.get('acquisitionSoftwareVersion','') |
| 1321 |
|
|
|
| 1322 |
|
|
def precursorPrecision(self,mz): |
| 1323 |
|
|
return 0 |
| 1324 |
|
|
|
| 1325 |
|
|
def precursorTune(self): |
| 1326 |
|
|
return False |
| 1327 |
|
|
|
| 1328 |
|
|
def lc(self): |
| 1329 |
|
|
return True |
| 1330 |
|
|
|
| 1331 |
|
|
def maldi(self): |
| 1332 |
|
|
return not self.lc() |
| 1333 |
|
|
|
| 1334 |
|
|
class AB4700T2D: |
| 1335 |
|
|
def __init__(self,filename,peaks=None): |
| 1336 |
|
|
self.filename = filename |
| 1337 |
|
|
self.datafiles = None |
| 1338 |
|
|
self.deapp = None |
| 1339 |
|
|
self.metadata = {} |
| 1340 |
|
|
self.platespots = {} |
| 1341 |
|
|
self.applyPeakDetect = [] |
| 1342 |
|
|
if peaks: |
| 1343 |
|
|
self.applyPeakDetect = map(int,peaks.split(',')) |
| 1344 |
|
|
|
| 1345 |
|
|
if not os.path.exists(self.filename): |
| 1346 |
|
|
print >>sys.stderr, "Filename %s does not exist."%(self.filename,) |
| 1347 |
|
|
sys.exit(1) |
| 1348 |
|
|
|
| 1349 |
|
|
self.filename = os.path.abspath(self.filename) |
| 1350 |
|
|
|
| 1351 |
|
|
self.dir = os.path.split(self.filename)[0] |
| 1352 |
|
|
|
| 1353 |
|
|
def __del__(self): |
| 1354 |
|
|
# Probably unnecessary |
| 1355 |
|
|
self.close() |
| 1356 |
|
|
|
| 1357 |
|
|
def open(self): |
| 1358 |
|
|
|
| 1359 |
|
|
if self.deapp is None: |
| 1360 |
|
|
|
| 1361 |
|
|
self.metadata['PLATEDEF'] = [] |
| 1362 |
|
|
self.metadata['PLATE'] = [] |
| 1363 |
|
|
self.metadata['SPOT'] = [] |
| 1364 |
|
|
self.metadata['SCAN'] = [] |
| 1365 |
|
|
|
| 1366 |
|
|
h = open(self.filename,'rb') |
| 1367 |
|
|
r = csv.reader(h,'excel-tab') |
| 1368 |
|
|
for l in r: |
| 1369 |
|
|
if len(l) == 0: |
| 1370 |
|
|
continue |
| 1371 |
|
|
kw = l.pop(0).upper() |
| 1372 |
|
|
if kw in ('PLATEDEF','PLATE','SPOT','SCAN'): |
| 1373 |
|
|
self.metadata[kw].append({}) |
| 1374 |
|
|
while len(l)>=2: |
| 1375 |
|
|
k = l.pop(0);v = l.pop(0); |
| 1376 |
|
|
if (kw == 'PLATE' and \ |
| 1377 |
|
|
(k in ('plateID','spotXCount','spotYCount','plateManufacturer','plateModel'))) or \ |
| 1378 |
|
|
(kw == 'PLATEDEF' and \ |
| 1379 |
|
|
(k in ('plateID','plateManufacturer','plateModel','spotNaming','maldiMatrix'))) or \ |
| 1380 |
|
|
(kw == 'SPOT' and \ |
| 1381 |
|
|
(k in ('plateID','spotID','spotXPosition','spotYPosition','maldiMatrix'))) or \ |
| 1382 |
|
|
(kw == 'SCAN' and \ |
| 1383 |
|
|
(k in ('plateID','spotID','filename','index'))): |
| 1384 |
|
|
self.metadata[kw][-1][k] = v |
| 1385 |
|
|
elif k == '': |
| 1386 |
|
|
break |
| 1387 |
|
|
else: |
| 1388 |
|
|
print >>sys.stderr,"Bad key %s for %s row"%(k,kw) |
| 1389 |
|
|
sys.exit(1) |
| 1390 |
|
|
h.close() |
| 1391 |
|
|
|
| 1392 |
|
|
for pd in self.metadata['PLATEDEF']: |
| 1393 |
|
|
# insert all the gory details needed for a particular plate model etc... |
| 1394 |
|
|
if pd['plateManufacturer'] == 'ABI / SCIEX' and pd['plateModel'] == '01-192+06-BB': |
| 1395 |
|
|
if not pd.has_key('spotNaming') or not pd.has_key('maldiMatrix') or \ |
| 1396 |
|
|
not pd['spotNaming'] in ('alpha','parallel','antiparallel'): |
| 1397 |
|
|
print >>sys.stderr,"Bad plate definition, missing maldiMatrix or spotNaming, or bad spotNaming value." |
| 1398 |
|
|
sys.exit(1) |
| 1399 |
|
|
self.metadata['PLATE'].append({ |
| 1400 |
|
|
'plateID':pd['plateID'], |
| 1401 |
|
|
'plateManufacturer':pd['plateManufacturer'], |
| 1402 |
|
|
'plateModel':pd['plateModel'], |
| 1403 |
|
|
'spotXCount':24, |
| 1404 |
|
|
'spotYCount':8, |
| 1405 |
|
|
}) |
| 1406 |
|
|
if pd['spotNaming'] == 'alpha': |
| 1407 |
|
|
for y in xrange(0,8): |
| 1408 |
|
|
for x in xrange(0,24): |
| 1409 |
|
|
self.metadata['SPOT'].append({ |
| 1410 |
|
|
'plateID':pd['plateID'], |
| 1411 |
|
|
'spotID':"%c%d"%(y+ord('A'),x+1), |
| 1412 |
|
|
'spotXPosition':x, |
| 1413 |
|
|
'spotYPosition':2*y+(x%2), |
| 1414 |
|
|
'maldiMatrix':pd['maldiMatrix'] |
| 1415 |
|
|
}) |
| 1416 |
|
|
else: |
| 1417 |
|
|
print >>sys.stderr,"Valid spotNaming value, not yet implemented." |
| 1418 |
|
|
sys.exit(1) |
| 1419 |
|
|
|
| 1420 |
|
|
for pl in self.metadata['PLATE']: |
| 1421 |
|
|
self.platespots[pl['plateID']] = [] |
| 1422 |
|
|
|
| 1423 |
|
|
for sp in self.metadata['SPOT']: |
| 1424 |
|
|
self.platespots[sp['plateID']].append(sp) |
| 1425 |
|
|
|
| 1426 |
|
|
self.datafiles = [ (os.path.join(self.dir,md['filename']),int(md['index'])) for md in self.metadata['SCAN'] ] |
| 1427 |
|
|
self.distinct_datafiles = dict([(os.path.join(self.dir,md['filename']), |
| 1428 |
|
|
fileSHA(os.path.join(self.dir,md['filename']))) for md in self.metadata['SCAN']]) |
| 1429 |
|
|
|
| 1430 |
|
|
self.maptoscan = {} |
| 1431 |
|
|
index = 0 |
| 1432 |
|
|
for md in self.metadata['SCAN']: |
| 1433 |
|
|
self.maptoscan[(os.path.join(self.dir,md['filename']),int(md['index']))] = index |
| 1434 |
|
|
index += 1 |
| 1435 |
|
|
|
| 1436 |
|
|
from win32com.client import Dispatch, gencache |
| 1437 |
|
|
self.deapp = Dispatch('DataExplorer.Application', |
| 1438 |
|
|
resultCLSID='{3FED40F1-D409-11D1-8B56-0060971CB54B}') |
| 1439 |
|
|
self.delib = gencache.EnsureModule('{06972F50-13F6-11D3-A5CB-0060971CB54B}',0,4,2) |
| 1440 |
|
|
self.deapp.AutomatedProcessing = 1 |
| 1441 |
|
|
self.deapp.Visible = 0 |
| 1442 |
|
|
|
| 1443 |
|
|
def close(self): |
| 1444 |
|
|
|
| 1445 |
|
|
if not self.deapp is None: |
| 1446 |
|
|
self.deapp.Quit() |
| 1447 |
|
|
self.deapp = None |
| 1448 |
|
|
|
| 1449 |
|
|
def peakDetect(self,msLevel): |
| 1450 |
|
|
return msLevel in self.applyPeakDetect |
| 1451 |
|
|
|
| 1452 |
|
|
# remove .set and .cts files to prevent DataExplorer crashes - DT 11-1-2006 |
| 1453 |
|
|
def remsettingsfile(self,fn): |
| 1454 |
nje01 |
1.2 |
# print "rmsettingsfile: %s"%fn |
| 1455 |
|
|
if ((len(fn) > 3) and (fn[-4:].lower() == '.t2d')): |
| 1456 |
|
|
path2del = fn[:-4] + '.cts' |
| 1457 |
|
|
if os.path.exists(path2del): |
| 1458 |
|
|
os.unlink(path2del) |
| 1459 |
|
|
path2del = fn[:-4] + '.set' |
| 1460 |
|
|
if os.path.exists(path2del): |
| 1461 |
|
|
os.unlink(path2del) |
| 1462 |
nje01 |
1.1 |
|
| 1463 |
|
|
def spectra(self): |
| 1464 |
|
|
self.open() |
| 1465 |
|
|
|
| 1466 |
|
|
prevfile = '' |
| 1467 |
|
|
for (f,i) in self.datafiles: |
| 1468 |
|
|
|
| 1469 |
|
|
if f != prevfile: |
| 1470 |
|
|
self.deapp.Documents.Close() |
| 1471 |
nje01 |
1.2 |
self.remsettingsfile(prevfile) |
| 1472 |
nje01 |
1.1 |
|
| 1473 |
|
|
if not os.path.exists(f): |
| 1474 |
|
|
print >>sys.stderr, "Filename %s does not exist."%(f,) |
| 1475 |
|
|
sys.exit(1) |
| 1476 |
|
|
|
| 1477 |
|
|
self.remsettingsfile(f) |
| 1478 |
nje01 |
1.2 |
self.deapp.Documents.Open(f) |
| 1479 |
|
|
# print "open %s"%f |
| 1480 |
nje01 |
1.1 |
|
| 1481 |
|
|
|
| 1482 |
|
|
doc = self.deapp.Documents.Item(0) |
| 1483 |
|
|
sv = doc.SpecView |
| 1484 |
|
|
|
| 1485 |
|
|
sv.SetSpectrumAt(i-1) |
| 1486 |
|
|
|
| 1487 |
|
|
(tf,fixedMass) = doc.InstrumentSettings.GetSetting(self.delib.constants.dePreCursorIon,i-1,None) |
| 1488 |
|
|
|
| 1489 |
|
|
if fixedMass > 0: |
| 1490 |
|
|
msLevel = 2 |
| 1491 |
|
|
else: |
| 1492 |
|
|
msLevel = 1 |
| 1493 |
|
|
|
| 1494 |
|
|
dataArr = array('f'); |
| 1495 |
|
|
peakDetect="False" |
| 1496 |
|
|
if self.peakDetect(msLevel): |
| 1497 |
|
|
peakDetect="True" |
| 1498 |
|
|
sv.CorrectBaseline() |
| 1499 |
|
|
doc.SpecSetup.NoiseReductionStdev = 2.0 |
| 1500 |
|
|
sv.FilterNoise(self.delib.constants.deNoiseRemoval) |
| 1501 |
|
|
sv.PeakSettings.PeakThresholdPercent = 1 |
| 1502 |
|
|
st,sp = sv.GetPeakData(self.delib.constants.deSpecPeakAll, |
| 1503 |
|
|
self.delib.constants.deSpecPeakSortMass, 0, 0) |
| 1504 |
|
|
for j in xrange(len(sp)): |
| 1505 |
|
|
x = sp[j][self.delib.constants.deSpecPeakCentroidMass] |
| 1506 |
|
|
y = sp[j][self.delib.constants.deSpecPeakArea] |
| 1507 |
|
|
if y <= 0: |
| 1508 |
|
|
continue |
| 1509 |
|
|
dataArr.append(x) |
| 1510 |
|
|
dataArr.append(y) |
| 1511 |
|
|
else: |
| 1512 |
|
|
n,s = sv.GetRawData(0,0) |
| 1513 |
|
|
for j in xrange(n): |
| 1514 |
|
|
dataArr.append(s[j][0]) |
| 1515 |
|
|
dataArr.append(s[j][1]) |
| 1516 |
|
|
|
| 1517 |
|
|
if len(dataArr) == 0: |
| 1518 |
|
|
continue |
| 1519 |
|
|
|
| 1520 |
|
|
polarity_val = "+" |
| 1521 |
|
|
|
| 1522 |
|
|
# Scan level attributes |
| 1523 |
|
|
# Required by mzXML (no format spec. needed) |
| 1524 |
nje01 |
1.3 |
d = {'msLevel':msLevel} |
| 1525 |
nje01 |
1.1 |
# Optional ('scan.' and prefixformat spec. needed) |
| 1526 |
|
|
d.update({ |
| 1527 |
|
|
'scan.polarity:%s':polarity_val, |
| 1528 |
|
|
}) |
| 1529 |
|
|
|
| 1530 |
|
|
scanindex = self.maptoscan[(f,i)] |
| 1531 |
|
|
d.update({ |
| 1532 |
|
|
'plateID':self.metadata['SCAN'][scanindex]['plateID'], |
| 1533 |
|
|
'spotID':self.metadata['SCAN'][scanindex]['spotID'], |
| 1534 |
|
|
}) |
| 1535 |
nje01 |
1.2 |
d.update({'scanOrigin.parentFileID:%s': self.distinct_datafiles[f], |
| 1536 |
nje01 |
1.1 |
'scanOrigin.num:%d': i}) |
| 1537 |
|
|
if msLevel == 1: |
| 1538 |
|
|
yield (dataArr,d) |
| 1539 |
|
|
else: |
| 1540 |
|
|
# tandem MS scans add the following |
| 1541 |
|
|
# Required by mzXML |
| 1542 |
|
|
d.update({'precursorMz':fixedMass}) |
| 1543 |
|
|
# Optional |
| 1544 |
|
|
d.update({'precursorMz.precursorCharge:%d':1}) |
| 1545 |
|
|
yield (dataArr,d) |
| 1546 |
|
|
|
| 1547 |
|
|
prevfile = f |
| 1548 |
|
|
|
| 1549 |
|
|
self.deapp.Documents.Close() |
| 1550 |
|
|
self.remsettingsfile(prevfile) |
| 1551 |
nje01 |
1.2 |
self.remsettingsfile(f) |
| 1552 |
nje01 |
1.1 |
|
| 1553 |
|
|
def getMsRunMetaData(self): |
| 1554 |
|
|
self.open() |
| 1555 |
|
|
return {} |
| 1556 |
|
|
|
| 1557 |
|
|
def getFilenames(self): |
| 1558 |
|
|
return [ t for t in self.distinct_datafiles.items() ] |
| 1559 |
|
|
|
| 1560 |
nje01 |
1.3 |
def msInstrumentID(self): |
| 1561 |
|
|
return "1" |
| 1562 |
|
|
|
| 1563 |
nje01 |
1.1 |
def msManufacturer(self): |
| 1564 |
|
|
return "ABI / SCIEX" |
| 1565 |
|
|
|
| 1566 |
|
|
def msModel(self): |
| 1567 |
|
|
return "4700 Proteomic Analyzer" |
| 1568 |
|
|
|
| 1569 |
|
|
def msIonisation(self): |
| 1570 |
|
|
return "MALDI" |
| 1571 |
|
|
|
| 1572 |
|
|
def msMassAnalyzer(self): |
| 1573 |
|
|
return "TOF" |
| 1574 |
|
|
|
| 1575 |
|
|
def msDetector(self): |
| 1576 |
nje01 |
1.3 |
return "LE" |
| 1577 |
nje01 |
1.1 |
|
| 1578 |
|
|
def acquisitionSoftware(self): |
| 1579 |
|
|
return "DataExplorer" |
| 1580 |
|
|
|
| 1581 |
|
|
def acquisitionSoftwareVersion(self): |
| 1582 |
|
|
return "1.0" |
| 1583 |
|
|
|
| 1584 |
|
|
def precursorPrecision(self,mz): |
| 1585 |
|
|
return .1 |
| 1586 |
|
|
|
| 1587 |
|
|
def precursorTune(self): |
| 1588 |
|
|
return False |
| 1589 |
|
|
|
| 1590 |
|
|
def lc(self): |
| 1591 |
|
|
return False |
| 1592 |
|
|
|
| 1593 |
|
|
def maldi(self): |
| 1594 |
|
|
return not self.lc() |
| 1595 |
|
|
|
| 1596 |
|
|
def plateData(self): |
| 1597 |
|
|
self.open() |
| 1598 |
|
|
for d in self.metadata['PLATE']: |
| 1599 |
|
|
yield d |
| 1600 |
|
|
|
| 1601 |
|
|
def spotData(self,plate): |
| 1602 |
|
|
self.open() |
| 1603 |
|
|
for s in self.platespots[plate]: |
| 1604 |
|
|
yield s |
| 1605 |
|
|
|
| 1606 |
|
|
class scanfilter: |
| 1607 |
|
|
def __init__(self,str): |
| 1608 |
|
|
self.rtre = re.compile('^PT([0-9]+(\.[0-9]+)?)S$') |
| 1609 |
|
|
self.intre = re.compile('^[1-9][0-9]*$') |
| 1610 |
|
|
self.floatre = re.compile('^[0-9]+(\.[0-9]+)?$') |
| 1611 |
|
|
self.cl = [] |
| 1612 |
|
|
clause = str.split(',') |
| 1613 |
|
|
for cl in clause: |
| 1614 |
|
|
scl = cl.split('.') |
| 1615 |
|
|
m = self.rtre.match(scl[2].strip()) |
| 1616 |
|
|
if m != None: |
| 1617 |
|
|
v = float(m.group(1)) |
| 1618 |
|
|
elif self.floatre.match(scl[2].strip()): |
| 1619 |
|
|
v = float(scl[2]) |
| 1620 |
|
|
elif self.intre.match(scl[2].strip()): |
| 1621 |
|
|
v = int(scl[2]) |
| 1622 |
|
|
else: |
| 1623 |
|
|
v = scl[2] |
| 1624 |
|
|
self.cl.append((scl[0],scl[1],v)) |
| 1625 |
|
|
|
| 1626 |
|
|
def test(self,d): |
| 1627 |
|
|
a = {} |
| 1628 |
|
|
for (k,v) in d.iteritems(): |
| 1629 |
|
|
k0 = k.split(':')[0].split('.')[-1] |
| 1630 |
|
|
a[k0] = v |
| 1631 |
|
|
for cl in self.cl: |
| 1632 |
|
|
if type(a[cl[0]]) == type(u'') or \ |
| 1633 |
|
|
type(a[cl[0]]) == type('') : |
| 1634 |
|
|
m = self.rtre.match(a[cl[0]].strip()) |
| 1635 |
|
|
if m != None: |
| 1636 |
|
|
v1 = float(m.group(1)) |
| 1637 |
|
|
elif self.floatre.match(a[cl[0]].strip()): |
| 1638 |
|
|
v1 = float(a[cl[0]]) |
| 1639 |
|
|
elif self.intre.match(a[cl[0]].strip()): |
| 1640 |
|
|
v1 = int(a[cl[0]]) |
| 1641 |
|
|
else: |
| 1642 |
|
|
v1 = a[cl[0]].strip() |
| 1643 |
|
|
else: |
| 1644 |
|
|
v1 = a[cl[0]] |
| 1645 |
|
|
v2 = cl[2] |
| 1646 |
|
|
# print >>sys.stderr, "Spectrum test:",v1,type(v1),cl[1],v2,type(v2) |
| 1647 |
|
|
# sys.stderr.flush() |
| 1648 |
|
|
if cl[1] == 'eq' and v1 != v2: |
| 1649 |
|
|
# print >>sys.stderr, "FALSE" |
| 1650 |
|
|
# sys.stderr.flush() |
| 1651 |
|
|
return False |
| 1652 |
|
|
elif cl[1] == 'ne' and not v1 != v2: |
| 1653 |
|
|
return False |
| 1654 |
|
|
elif cl[1] == 'lt' and not v1 < v2: |
| 1655 |
|
|
return False |
| 1656 |
|
|
elif cl[1] == 'le' and not v1 <= v2: |
| 1657 |
|
|
return False |
| 1658 |
|
|
elif cl[1] == 'gt' and not v1 > v2: |
| 1659 |
|
|
return False |
| 1660 |
|
|
elif cl[1] == 'ge' and not v1 >= v2: |
| 1661 |
|
|
return False |
| 1662 |
|
|
# print >>sys.stderr, "TRUE" |
| 1663 |
|
|
# sys.stderr.flush() |
| 1664 |
|
|
return True |
| 1665 |
|
|
|
| 1666 |
|
|
if __name__ == '__main__': |
| 1667 |
|
|
|
| 1668 |
|
|
from optparse import OptionParser |
| 1669 |
|
|
import sys |
| 1670 |
|
|
import glob |
| 1671 |
|
|
|
| 1672 |
|
|
parser = OptionParser() |
| 1673 |
|
|
parser.add_option("-R", "--rawdata", type="string", dest="rawdata", default="",\ |
| 1674 |
|
|
help="Format of raw data. Optional if raw spectra file ends in .wiff or .t2m.") |
| 1675 |
|
|
parser.add_option("-X", "--xmlformat", type="string", dest="xmlformat", default="",\ |
| 1676 |
|
|
help="XML format to output. Optional if output file ends in .mzxml or .mzdata.") |
| 1677 |
|
|
parser.add_option("-o", "--output", type="string", dest="output", default="",\ |
| 1678 |
|
|
help="Output file.") |
| 1679 |
|
|
parser.add_option("-p", "--peaks", type="string", dest="peaks", default="2",\ |
| 1680 |
|
|
help="Level(s) of spectra to apply peak detection to (comma separated). QStar,4700 only.") |
| 1681 |
|
|
parser.add_option("-f", "--filter", type="string", dest="filter", default=None,\ |
| 1682 |
|
|
help="Filter on mzxml scan meta-data: field.op.value[,field.op.value]. Default: No filter.") |
| 1683 |
nje01 |
1.3 |
parser.add_option("-V", "--version", type='string', dest="version", default="3.0", |
| 1684 |
|
|
help="XML version. mzXML only. Valid options '2.1','2.2','3.0'. Default: '3.0'.") |
| 1685 |
|
|
parser.add_option("-z", "--compress_peaks", action="store_true", dest="compress_peaks", default=None,\ |
| 1686 |
|
|
help="Compress mzXML peaks data using zlib. Default: False") |
| 1687 |
|
|
parser.add_option("-Z", "--compress", type="string", dest="compress", default=None,\ |
| 1688 |
|
|
help="Compress output file. Valid options 'gz'. Default: None.") |
| 1689 |
nje01 |
1.1 |
parser.add_option("-d", "--debug", action="store_true", dest="debug", default=False,\ |
| 1690 |
|
|
help="Debug. First 10 spectra only, and truncated peaks data element. Default: False.") |
| 1691 |
|
|
|
| 1692 |
|
|
( opts, args ) = parser.parse_args() |
| 1693 |
|
|
|
| 1694 |
|
|
if opts.output == "" and opts.xmlformat == "": |
| 1695 |
|
|
parser.error("Either -o or -X must be suppied.") |
| 1696 |
|
|
sys.exit(1) |
| 1697 |
|
|
|
| 1698 |
|
|
if opts.filter != None: |
| 1699 |
|
|
filt=scanfilter(opts.filter) |
| 1700 |
|
|
else: |
| 1701 |
|
|
filt=None |
| 1702 |
|
|
|
| 1703 |
|
|
argsglob = [] |
| 1704 |
|
|
for a in args: |
| 1705 |
|
|
argsglob.extend(glob.glob(a)) |
| 1706 |
|
|
|
| 1707 |
|
|
if opts.output != "" and len(argsglob) > 1: |
| 1708 |
|
|
parser.error("At most one raw spectrum data file is permitted, if -o option is used.") |
| 1709 |
|
|
|
| 1710 |
|
|
for a in argsglob: |
| 1711 |
|
|
|
| 1712 |
|
|
if opts.output != "": |
| 1713 |
|
|
o = opts.output |
| 1714 |
|
|
else: |
| 1715 |
|
|
p = a.rfind('.') |
| 1716 |
|
|
o = a[0:p]+'.'+opts.xmlformat |
| 1717 |
|
|
|
| 1718 |
|
|
if o == a: |
| 1719 |
|
|
print >>sys.stderr, "Input file %s and output file %s are the same!"%(a,o) |
| 1720 |
|
|
sys.exit(1) |
| 1721 |
|
|
|
| 1722 |
|
|
print >>sys.stderr, "Processing",a,"to",o |
| 1723 |
|
|
|
| 1724 |
|
|
if opts.rawdata.lower() in ('wiff','qstar'): |
| 1725 |
|
|
r = QStarWiff(a,opts.peaks) |
| 1726 |
|
|
elif opts.rawdata.lower() in ('t2d','dat','ab4700','ab4800','mariner','voyager'): |
| 1727 |
|
|
r = AB4700T2D(a,opts.peaks) |
| 1728 |
|
|
elif opts.rawdata.lower() in ('mzxml',): |
| 1729 |
|
|
r = FromMzXML(a) |
| 1730 |
|
|
elif a[-5:].lower() in ('.wiff',): |
| 1731 |
|
|
r = QStarWiff(a,opts.peaks) |
| 1732 |
|
|
elif a[-4:].lower() in ('.t2m',): |
| 1733 |
|
|
r = AB4700T2D(a,opts.peaks) |
| 1734 |
|
|
elif a[-6:].lower() in ('.mzxml',): |
| 1735 |
|
|
r = FromMzXML(a) |
| 1736 |
|
|
else: |
| 1737 |
|
|
parser.error("Bad rawdata format specification.") |
| 1738 |
|
|
sys.exit(1) |
| 1739 |
|
|
|
| 1740 |
|
|
if opts.xmlformat.lower() == 'mzxml': |
| 1741 |
nje01 |
1.3 |
x = ToMzXML(r,o,opts.compress,filt,opts.compress_peaks,opts.version) |
| 1742 |
nje01 |
1.1 |
elif opts.xmlformat.lower() == 'mzdata': |
| 1743 |
|
|
x = ToMzData(r,o,opts.compress,filt) |
| 1744 |
|
|
elif opts.output[-6:].lower() in ('.mzxml',): |
| 1745 |
nje01 |
1.3 |
x = ToMzXML(r,opts.output,opts.compress,filt,opts.compress_peaks,opts.version) |
| 1746 |
nje01 |
1.1 |
elif opts.output[-7:].lower() in ('.mzdata',): |
| 1747 |
|
|
x = ToMzData(r,opts.output,opts.compress,filt) |
| 1748 |
|
|
else: |
| 1749 |
|
|
parser.error("Bad xml format specification.") |
| 1750 |
|
|
sys.exit(1) |
| 1751 |
|
|
|
| 1752 |
|
|
x.write(debug=opts.debug) |
