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1 #
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2 # Developed by Praveen Kumar
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3 # Galaxy-P Team (Griffin's Lab)
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4 # University of Minnesota
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5 #
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6 #
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7
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8 def main():
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9 from pyteomics import mzml
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10 import os
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11 import sys
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12 import shutil
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13 import subprocess
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14 import re
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15 import pandas as pd
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16 from operator import itemgetter
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17 from itertools import groupby
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18 if len(sys.argv) >= 5:
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19 # Start of Reading Scans from PSM file
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20 # Creating dictionary of PSM file: key = filename key = list of scan numbers
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21 ScanFile = sys.argv[2]
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22 spectrumTitleList = list(pd.read_csv(ScanFile, "\t")['Spectrum Title'])
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23 scanFileNumber = [[".".join(each.split(".")[:-3]), int(each.split(".")[-2:-1][0])] for each in spectrumTitleList]
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24 scanDict = {}
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25 for each in scanFileNumber:
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26 if scanDict.has_key(each[0]):
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27 scanDict[each[0]].append(int(each[1]))
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28 else:
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29 scanDict[each[0]] = [int(each[1])]
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30 # End of Reading Scans from PSM file
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31
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32 inputPath = sys.argv[1]
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33 ##outPath = "/".join(sys.argv[3].split("/")[:-1])
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34 outPath = sys.argv[3]
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35 ##outFile = sys.argv[3].split("/")[-1]
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36 allScanList = []
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37
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38 # Read all scan numbers using indexedmzML/indexList/index/offset tags
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39 for k in mzml.read(inputPath).iterfind('indexedmzML/indexList/index/offset'):
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40 if re.search("scan=(\d+)", k['idRef']):
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41 a = re.search("scan=(\d+)", k['idRef'])
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42 allScanList.append(int(a.group(1)))
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43 # End of Reading mzML file
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44
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45 fraction_name = sys.argv[4]
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46 if scanDict.has_key(fraction_name):
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47 scan2remove = scanDict[fraction_name]
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48 else:
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49 scan2remove = []
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50 scan2retain = list(set(allScanList) - set(scan2remove))
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51 scan2retain.sort()
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52 scansRemoved = list(set(allScanList) - set(scan2retain))
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53 # scan2retain contains scans that is to be retained
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54
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55 # Print Stats
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56 print >> sys.stdout,"Total number of Scan Numbers: %d" % len(list(set(allScanList)))
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57 print >> sys.stdout,"Number of Scans to remove: %d" % len(list(set(scan2remove)))
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58 print >> sys.stdout,"Number of Scans retained: %d" % len(scan2retain)
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59 print >> sys.stdout,"Number of Scans removed: %d" % len(scansRemoved)
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60
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61
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62 # Identifying groups of continuous numbers in the scan2retain and creating scanString
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63 scanString = ""
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64 for a, b in groupby(enumerate(scan2retain), lambda(i,x):i-x):
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65 x = map(itemgetter(1), b)
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66 scanString = scanString + "["+str(x[0])+","+str(x[-1])+"] "
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67 # end identifying
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68
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69 # start create filter file
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70 filter_file = open("filter.txt", "w")
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71 filter_file.write("filter=scanNumber %s\n" % scanString)
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72 filter_file.close()
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73 # end create filter file
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74
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75 # Prepare command for msconvert
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76 inputFile = fraction_name+".mzML"
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77 os.symlink(inputPath,inputFile)
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78 outFile = "filtered_"+fraction_name+".mzML"
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79 # msconvert_command = "msconvert " + inputFile + " --filter " + "\"scanNumber " + scanString + " \" " + " --outfile " + outFile + " --mzML --zlib"
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80 msconvert_command = "msconvert " + inputFile + " -c filter.txt " + " --outfile " + outFile + " --mzML --zlib"
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81
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82
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83 # Run msconvert
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84 try:
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85 subprocess.check_output(msconvert_command, stderr=subprocess.STDOUT, shell=True)
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86 except subprocess.CalledProcessError as e:
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87 sys.stderr.write( "msconvert resulted in error: %s: %s" % ( e.returncode, e.output ))
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88 sys.exit(e.returncode)
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89 # Copy output to
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90 shutil.copyfile(outFile, outPath)
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91
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92 else:
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93 print "Please contact the admin. Number of inputs are not sufficient to run the program.\n"
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94
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95 if __name__ == "__main__":
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96 main()
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97
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98
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