annotate ipapy2_MS2_annotation.py @ 0:428abc41a101 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
author recetox
date Fri, 16 May 2025 08:01:46 +0000
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1 from ipaPy2 import ipa
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2 from utils import flattern_annotations, MSArgumentParser
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3
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4
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5 def main(
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6 input_dataset_mapped_isotope_patterns,
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7 input_dataset_MS2,
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8 input_dataset_adducts,
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9 input_dataset_MS2_DB,
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10 ppm,
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11 ratiosd,
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12 ppmunk,
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13 ratiounk,
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14 ppmthr,
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15 pRTNone,
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16 pRTout,
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17 mzdCS,
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18 ppmCS,
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19 CSunk,
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20 evfilt,
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21 output_dataset,
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22 ncores,
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23 ):
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24 annotations = ipa.MSMSannotation(
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25 input_dataset_mapped_isotope_patterns,
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26 input_dataset_MS2,
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27 input_dataset_adducts,
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28 input_dataset_MS2_DB,
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29 ppm=ppm,
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30 ratiosd=ratiosd,
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31 ppmunk=ppmunk,
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32 ratiounk=ratiounk,
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33 ppmthr=ppmthr,
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34 pRTNone=pRTNone,
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35 pRTout=pRTout,
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36 mzdCS=mzdCS,
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37 ppmCS=ppmCS,
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38 CSunk=CSunk,
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39 evfilt=evfilt,
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40 ncores=ncores,
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41 )
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42 annotations_flat = flattern_annotations(annotations)
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43 write_func, file_path = output_dataset
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44 write_func(annotations_flat, file_path)
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45
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46
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47 if __name__ == "__main__":
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48 parser = MSArgumentParser(
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49 """Annotation of the dataset base on the MS1 and MS2 information. Prior
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50 probabilities are based on mass only, while post probabilities are based
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51 on mass, RT, previous knowledge and isotope patterns."""
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52 )
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53 parser.add_argument(
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54 "--input_dataset_mapped_isotope_patterns",
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55 nargs=2,
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56 action="load_data",
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57 required=True,
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58 help=(
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59 "A dataset containing the MS1 data. Ideally obtained from"
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60 " map_isotope_patterns"
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61 ),
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62 )
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63 parser.add_argument(
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64 "--input_dataset_MS2",
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65 nargs=2,
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66 action="load_data",
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67 required=True,
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68 help="A dataset containing the MS2 fragmentation data",
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69 )
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70 parser.add_argument(
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71 "--input_dataset_adducts",
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72 nargs=2,
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73 action="load_data",
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74 required=True,
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75 help=(
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76 "A dataset containing the information on all the possible adducts given the"
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77 " database. Ideally obtained from compute_all_adducts"
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78 ),
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79 )
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80 parser.add_argument(
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81 "--input_dataset_MS2_DB",
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82 nargs=2,
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83 action="load_data",
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84 required=True,
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85 help="A dataset containing the MS2 database",
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86 )
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87 parser.add_argument(
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88 "--mzdCS",
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89 type=int,
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90 default=0,
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91 help="""maximum mz difference allowed when computing cosine similarity
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92 scores. If one wants to use this parameter instead of ppmCS, this
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93 must be set to 0. Default 0.""",
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94 )
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95 parser.add_argument(
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96 "--ppmCS",
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97 type=int,
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98 default=10,
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99 help="""maximum ppm allowed when computing cosine similarity scores.
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100 If one wants to use this parameter instead of mzdCS, this must be
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101 set to 0. Default 10.""",
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102 )
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103 parser.add_argument(
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104 "--CSunk",
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105 type=float,
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106 default=0.7,
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107 help="""cosine similarity score associated with the 'unknown' annotation.
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108 Default 0.7""",
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109 )
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110 parser.add_argument(
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111 "--evfilt",
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112 type=bool,
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113 default=False,
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114 help="""Default value False. If true, only spectrum acquired with the same
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115 collision energy are considered.""",
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116 )
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117 args = parser.parse_args()
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118 main(
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119 args.input_dataset_mapped_isotope_patterns,
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120 args.input_dataset_MS2,
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121 args.input_dataset_adducts,
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122 args.input_dataset_MS2_DB,
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123 args.ppm,
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124 args.ratiosd,
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125 args.ppmunk,
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126 args.ratiounk,
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127 args.ppmthr,
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128 args.pRTNone,
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129 args.pRTout,
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130 args.mzdCS,
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131 args.ppmCS,
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132 args.CSunk,
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133 args.evfilt,
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134 args.output_dataset,
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135 args.ncores,
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136 )