--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MSMS_Extractor.py	Mon Feb 13 02:44:05 2017 -0500
@@ -0,0 +1,100 @@
+# 
+# Developed by Praveen Kumar
+# Galaxy-P Team (Griffin's Lab)
+# University of Minnesota
+#
+#
+
+def main():
+    from pyteomics import mzml
+    import os
+    import sys
+    import shutil
+    import subprocess
+    import re
+    import pandas as pd
+    from operator import itemgetter
+    from itertools import groupby
+    if len(sys.argv) >= 5:
+        # Start of Reading Scans from PSM file
+        # Creating dictionary of PSM file: key = filename key = list of scan numbers
+        ScanFile = sys.argv[2]
+        spectrumTitleList = list(pd.read_csv(ScanFile, "\t")['Spectrum Title'])
+        scanFileNumber = [[".".join(each.split(".")[:-3]), int(each.split(".")[-2:-1][0])] for each in spectrumTitleList]
+        scanDict = {}
+        for each in scanFileNumber:
+            if scanDict.has_key(each[0]):
+                scanDict[each[0]].append(int(each[1]))
+            else:
+                scanDict[each[0]] = [int(each[1])]
+        # End of Reading Scans from PSM file
+        
+        inputPath = sys.argv[1]
+        ##outPath = "/".join(sys.argv[3].split("/")[:-1])
+        outPath = sys.argv[3]
+        ##outFile = sys.argv[3].split("/")[-1]
+        allScanList = []
+        
+        # Read all scan numbers using indexedmzML/indexList/index/offset tags
+        for k in mzml.read(inputPath).iterfind('indexedmzML/indexList/index/offset'):
+            if re.search("scan=(\d+)", k['idRef']):
+                a = re.search("scan=(\d+)", k['idRef'])
+                allScanList.append(int(a.group(1)))
+        # End of Reading mzML file
+        
+        fraction_name = sys.argv[4]
+        if scanDict.has_key(fraction_name):
+            scan2remove = scanDict[fraction_name]
+        else:
+            scan2remove = []
+        scan2retain = list(set(allScanList) - set(scan2remove))
+        scan2retain.sort()
+        scansRemoved = list(set(allScanList) - set(scan2retain))
+        # scan2retain contains scans that is to be retained
+        
+        # Print Stats
+        print >> sys.stdout,"Total number of Scan Numbers: %d" % len(list(set(allScanList)))
+        print >> sys.stdout,"Number of Scans to remove: %d" % len(list(set(scan2remove)))
+        print >> sys.stdout,"Number of Scans retained: %d" % len(scan2retain)
+        print >> sys.stdout,"Number of Scans removed: %d" % len(scansRemoved)
+        
+        
+        # Identifying groups of continuous numbers in the scan2retain and creating scanString
+        scanString = ""
+        for a, b in groupby(enumerate(scan2retain), lambda(i,x):i-x):
+            x = map(itemgetter(1), b)
+            scanString = scanString + "["+str(x[0])+","+str(x[-1])+"] "
+        # end identifying
+        
+        # start create filter file
+        filter_file = open("filter.txt", "w")
+        filter_file.write("filter=scanNumber %s\n" % scanString)
+        filter_file.close()
+        # end create filter file 
+        
+        # Prepare command for msconvert
+        inputFile = fraction_name+".mzML"
+        os.symlink(inputPath,inputFile)
+        outFile = "filtered_"+fraction_name+".mzML"
+        # msconvert_command = "msconvert " + inputFile + " --filter " + "\"scanNumber " + scanString + " \" " + " --outfile " + outFile + " --mzML --zlib"
+        msconvert_command = "msconvert " + inputFile + " -c filter.txt " + " --outfile " + outFile + " --mzML --zlib"
+        
+        
+        # Run msconvert
+        try:
+            subprocess.check_output(msconvert_command, stderr=subprocess.STDOUT, shell=True)
+        except subprocess.CalledProcessError as e:
+            sys.stderr.write( "msconvert resulted in error: %s: %s" % ( e.returncode, e.output ))
+            sys.exit(e.returncode)
+        # Copy output to 
+        shutil.copyfile(outFile, outPath)
+        
+    else:
+        print "Please contact the admin. Number of inputs are not sufficient to run the program.\n"
+
+if __name__ == "__main__":
+    main()
+    
+    
+    
+