Mercurial > repos > galaxyp > msms_extractor

annotate msms_extractor.py @ 0:4bef80b09854 draft default tip

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"planemo upload commit 498440b547e1feaa6a81764b55ac8208626d70a8"
author galaxyp
date Tue, 29 Oct 2019 11:09:46 -0400
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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
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9
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10 from pyteomics import mzml
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11 import os
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12 import sys
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13 import shutil
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14 import subprocess
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15 import re
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16 import pandas as pd
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17 from operator import itemgetter
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18 from itertools import groupby
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19 import random
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20 import argparse
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21
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22 def main():
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23 if len(sys.argv) >= 7:
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24 parser = argparse.ArgumentParser()
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25 parser.add_argument("msms", help="mzML File")
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26 parser.add_argument("psm", help="PSM Report File")
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27 parser.add_argument("out", help="Output filename")
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28 parser.add_argument("filestring", help="MSMS File string as identifier")
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29 parser.add_argument("remove_retain", help="Remove scans reported in the PSM report")
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30 parser.add_argument("random", help="Random MSMS scans used with to use with --retain (default=0)", default=0)
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31 args = parser.parse_args()
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32 # Start of Reading Scans from PSM file
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33 # Creating dictionary of PSM file: key = filename key = list of scan numbers
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34
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35 # removeORretain = sys.argv[5].strip()
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36 # randomScans = int(sys.argv[6].strip())
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37
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38 removeORretain = args.remove_retain
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39 randomScans = int(args.random)
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40
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41
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42 # ScanFile = sys.argv[2]
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43 ScanFile = args.psm
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44 spectrumTitleList = list(pd.read_csv(ScanFile, "\t")['Spectrum Title'])
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45 scanFileNumber = [[".".join(each.split(".")[:-3]), int(each.split(".")[-2:-1][0])] for each in spectrumTitleList]
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46 scanDict = {}
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47 for each in scanFileNumber:
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48 if each[0] in scanDict.keys():
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49 scanDict[each[0]].append(int(each[1]))
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50 else:
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51 scanDict[each[0]] = [int(each[1])]
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52 # End of Reading Scans from PSM file
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53
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54 # inputPath = sys.argv[1]
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55 inputPath = args.msms
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56 ##outPath = "/".join(sys.argv[3].split("/")[:-1])
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57 # outPath = sys.argv[3]
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58 outPath = args.out
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59 ##outFile = sys.argv[3].split("/")[-1]
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60 allScanList = []
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61 # Read all scan numbers using indexedmzML/indexList/index/offset tags
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62 for k in mzml.read(inputPath).iterfind('indexedmzML/indexList/index/offset'):
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63 if re.search("scan=(\d+)", k['idRef']):
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64 a = re.search("scan=(\d+)", k['idRef'])
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65 allScanList.append(int(a.group(1)))
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66 allScanList = list(set(allScanList))
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67 # End of Reading mzML file
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68 # fraction_name = sys.argv[4]
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69 fraction_name = args.filestring
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70 if fraction_name in scanDict.keys():
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71 scansInList = scanDict[fraction_name]
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72 else:
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73 scansInList = []
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74 scansNotInList = list(set(allScanList) - set(scansInList))
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75 flag = 0
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76 if removeORretain == "remove":
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77 scan2retain = scansNotInList
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78 scan2retain = list(set(scan2retain))
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79 scan2retain.sort()
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80 scansRemoved = scansInList
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81 # scan2retain contains scans that is to be retained
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82 elif removeORretain == "retain" and randomScans < len(scansNotInList):
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83 # Randomly select spectra
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84 random_scans = random.sample(scansNotInList, randomScans)
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85
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86 scan2retain = random_scans + scansInList
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87 scan2retain = list(set(scan2retain))
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88 scan2retain.sort()
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89 scansRemoved = list(set(allScanList) - set(scan2retain))
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90 # scan2retain contains scans that is to be retained
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91 else:
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92 flag = 1
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93
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94 if flag == 1:
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95 scan2retain = scansInList
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96 scan2retain = list(set(scan2retain))
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97 scan2retain.sort()
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98 scansRemoved = list(set(allScanList) - set(scan2retain))
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99
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100 # scan2retain contains scans that is to be retained
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101 print("ERROR: Number of Random Scans queried is more than available. The result has provided zero random scans.", file=sys.stdout)
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102 print("Number of available scans for random selection: " + str(len(scansNotInList)), file=sys.stdout)
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103 print("Try a number less than the available number. Thanks!!", file=sys.stdout)
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104 print("Number of Scans retained: " + str(len(scan2retain)), file=sys.stdout)
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105 else:
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106 # Print Stats
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107 print("Total number of Scan Numbers: " + str(len(list(set(allScanList)))), file=sys.stdout)
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108 print("Number of Scans retained: " + str(len(scan2retain)), file=sys.stdout)
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109 print("Number of Scans removed: " + str(len(scansRemoved)), file=sys.stdout)
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110
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111
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112 # Identifying groups of continuous numbers in the scan2retain and creating scanString
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113 scanString = ""
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114 for a, b in groupby(enumerate(scan2retain), lambda x:x[1]-x[0]):
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115 x = list(map(itemgetter(1), b))
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116 scanString = scanString + "["+str(x[0])+","+str(x[-1])+"] "
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117 # end identifying
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118 # start create filter file
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119 filter_file = open("filter.txt", "w")
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120 filter_file.write("filter=scanNumber %s\n" % scanString)
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121 filter_file.close()
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122 # end create filter file
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123
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124 # Prepare command for msconvert
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125 inputFile = fraction_name+".mzML"
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126 os.symlink(inputPath,inputFile)
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127 outFile = "filtered_"+fraction_name+".mzML"
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128 # msconvert_command = "msconvert " + inputFile + " --filter " + "\"scanNumber " + scanString + " \" " + " --outfile " + outFile + " --mzML --zlib"
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129 msconvert_command = "msconvert " + inputFile + " -c filter.txt " + " --outfile " + outFile + " --mzML --zlib"
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130
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131
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132 # Run msconvert
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133 try:
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134 subprocess.check_output(msconvert_command, stderr=subprocess.STDOUT, shell=True)
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135 except subprocess.CalledProcessError as e:
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136 sys.stderr.write( "msconvert resulted in error: %s: %s" % ( e.returncode, e.output ))
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137 sys.exit(e.returncode)
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138 # Copy output to
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139 shutil.copyfile(outFile, outPath)
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140 else:
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141 print("Please contact the admin. Number of inputs are not sufficient to run the program.\n")
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142
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143 if __name__ == "__main__":
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144 main()
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145
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146
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147
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148