Pull Request for the Algorithm Comparison Tool #4
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| #Author: Mihai Avram - [email protected] | ||
| #Date: 3/15/2017 | ||
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| import sys | ||
| import argparse | ||
| import pandas as pd | ||
| import numpy as np | ||
| import string | ||
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| def main(): | ||
| parser = argparse.ArgumentParser() | ||
| #Required parameters -a1 and -a2 which denote the paths to the two input algorithm files to be compared (print output to the console) | ||
| parser.add_argument("-a1", "--alg1file", type=str, help="the relative or absolute location and name of the input file of the first algorithm", required=True) | ||
| parser.add_argument("-a2", "--alg2file", type=str, help="the relative or absolute location and name of the input file of the second algorithm", required=True) | ||
| #Optional parameters -oc, -oa1, -oa2 which denote output paths for the comparisons (print output to these files) | ||
| parser.add_argument("-oc", "--outputcomparison", type=str, help="the relative or absolute location and name of the alg1/alg2 comparison output file (.txt extension recommended)", default="CompOutputDefault.txt") | ||
| parser.add_argument("-oa1", "--alg1confusion", type=str, help="the relative or absolute location and name of the alg1 confusion result output file (.csv extension recommended)", default="Alg1OutConfDefault.csv") | ||
| parser.add_argument("-oa2", "--alg2confusion", type=str, help="the relative or absolute location and name of the alg2 confusion result output file (.csv extension recommended)", default="Alg2OutConfDefault.csv") | ||
| args = parser.parse_args() | ||
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| computeAndPrint(args.alg1file, args.alg2file, args.outputcomparison, args.alg1confusion, args.alg2confusion) | ||
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| def computeAndPrint(alg1file, alg2file, outputcomparison, alg1confusion, alg2confusion): | ||
| #Importing algorithms to be compared | ||
| try: | ||
| alg1 = pd.read_csv(alg1file) | ||
| alg2 = pd.read_csv(alg2file) | ||
| except: | ||
| print("Error reading the alg1 and alg2 input files, please ensure file path and file format is correct.", file=sys.stderr) | ||
| sys.exit(1) | ||
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| #Alg1 checking for null values in pertinent columns | ||
| if any(pd.isnull(alg1['sid'])) or any(pd.isnull(alg1['oid'])) or any(pd.isnull(alg1['class'])) or any(pd.isnull(alg1['score'])): | ||
| print("There are missing column values in the sid, oid, class, or score columns in alg1", file=sys.stderr) | ||
| sys.exit(1) | ||
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| #Alg2 checking for null values in pertinent columns | ||
| if any(pd.isnull(alg2['sid'])) or any(pd.isnull(alg2['oid'])) or any(pd.isnull(alg2['class'])) or any(pd.isnull(alg2['score'])): | ||
| print("There are missing column values in the sid, oid, class, or score columns in alg2", file=sys.stderr) | ||
| sys.exit(1) | ||
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| #Algorithm comparison | ||
| #Preparatory work | ||
| alg1 = alg1.sort_values(['sid','score'], axis=0, ascending=False) | ||
| alg2 = alg2.sort_values(['sid','score'], axis=0, ascending=False) | ||
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| alg1DistinctObjNum = len(alg1.oid.unique()) | ||
| alg2DistinctObjNum = len(alg2.oid.unique()) | ||
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| idColLocation = alg1.columns.get_loc('sid') | ||
| subjectColLocation = alg1.columns.get_loc('sub') | ||
| objectIDColLocation = alg1.columns.get_loc('oid') | ||
| objectColLocation = alg1.columns.get_loc('obj') | ||
| classColLocation = alg1.columns.get_loc('class') | ||
| scoreColLocation = alg1.columns.get_loc('score') | ||
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| correctPredAlg1 = {} | ||
| incorrectPredAlg1 = {} | ||
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| correctPredAlg2 = {} | ||
| incorrectPredAlg2 = {} | ||
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| #Creating Dictionary of id/subject matches | ||
| idSubjectMapping = {} | ||
| for index, row in alg1.iterrows(): | ||
| idSubjectMapping[row[subjectColLocation]] = row[idColLocation] | ||
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| #Comparisons | ||
| for sample in range(0, alg1.shape[0], alg1DistinctObjNum): | ||
| if alg1.iloc[sample, classColLocation] == 1: | ||
| correctPredAlg1[str(alg1.iloc[sample, subjectColLocation])] = alg1.iloc[sample, scoreColLocation] | ||
| elif alg1.iloc[sample, classColLocation] == 0: | ||
| incorrectPredAlg1[str(alg1.iloc[sample, subjectColLocation])] = alg1.iloc[sample, scoreColLocation] | ||
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| for sample in range(0, alg2.shape[0], alg2DistinctObjNum): | ||
| if alg2.iloc[sample, classColLocation] == 1: | ||
| correctPredAlg2[str(alg2.iloc[sample, subjectColLocation])] = alg2.iloc[sample, scoreColLocation] | ||
| elif alg2.iloc[sample, classColLocation] == 0: | ||
| incorrectPredAlg2[str(alg2.iloc[sample, subjectColLocation])] = alg2.iloc[sample, scoreColLocation] | ||
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| #if the 3 output files were not specified, print results to console, if only one was specified, use that one and default locations for the others | ||
| if outputcomparison == "CompOutputDefault.txt" and alg1confusion == "Alg1OutConfDefault.csv" and alg2confusion == "Alg2OutConfDefault.csv": | ||
| #Printing Results (comparisonPrint function used for this) | ||
| def comparisonPrint(algorithm): | ||
| for subject, score in algorithm.items(): | ||
| print("ID:", idSubjectMapping[subject], "- Subject:", subject.replace("dbr:",""), "with score", score) | ||
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| print("\nALG1 CORRECTLY PREDICTED THE FOLLOWING") | ||
| comparisonPrint(correctPredAlg1) | ||
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| print("\nALG1 INCORRECTLY PREDICTED THE FOLLOWING") | ||
| comparisonPrint(incorrectPredAlg1) | ||
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| print("\nALG2 CORRECTLY PREDICTED THE FOLLOWING") | ||
| comparisonPrint(correctPredAlg2) | ||
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| print("\nALG2 INCORRECTLY PREDICTED THE FOLLOWING") | ||
| comparisonPrint(incorrectPredAlg2) | ||
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| bothCorrect = set(correctPredAlg1.keys()) & set(correctPredAlg2.keys()) | ||
| bothIncorrect = set(incorrectPredAlg1.keys()) & set(incorrectPredAlg2.keys()) | ||
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| alg1Correctalg2Incorrect = set(correctPredAlg1.keys()) & set(incorrectPredAlg2.keys()) | ||
| alg2Correctalg1Incorrect = set(correctPredAlg2.keys()) & set(incorrectPredAlg1.keys()) | ||
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| print("\nINSTANCES WHERE ALG1 PREDICTED CORRECTLY BUT ALG2 DIDN'T") | ||
| for instance in alg1Correctalg2Incorrect: | ||
| print("ID:",idSubjectMapping[instance], "- Subject:", instance.replace("dbr:","")) | ||
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| print("\nINSTANCES WHERE ALG2 PREDICTED CORRECTLY BUT ALG1 DIDN'T") | ||
| for instance in alg2Correctalg1Incorrect: | ||
| print("ID:",idSubjectMapping[instance], "- Subject:", instance.replace("dbr:","")) | ||
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| #Comparison of algorithms for when both predicted correctly | ||
| print("\nCOMPARISON OF ALGS WHEN BOTH PREDICTED CORRECTLY") | ||
| for subject in bothCorrect: | ||
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| alg1CompSegment = alg1[alg1['sub'] == subject] | ||
| alg2CompSegment = alg2[alg2['sub'] == subject] | ||
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| #Same prediction level, so must compare ratios between our first correct prediction, and the next prediction | ||
| alg1Ratio = alg1CompSegment.iloc[0,scoreColLocation]/alg1CompSegment.iloc[1,scoreColLocation] | ||
| alg2Ratio = alg2CompSegment.iloc[0,scoreColLocation]/alg2CompSegment.iloc[1,scoreColLocation] | ||
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| #The greater the ratio the better the prediction, i.e. | ||
| #0.5 (our prediction) 0.04 (next prediction) vs. | ||
| #0.5 (our prediction) 0.4 (next prediction) | ||
| if alg1Ratio > alg2Ratio: | ||
| print("Alg1 > Alg2 for relation:", "ID:", idSubjectMapping[subject], "- Subject:", subject.replace("dbr:","")) | ||
| elif alg1Ratio < alg2Ratio: | ||
| print("Alg1 < Alg2 for relation:", "ID:", idSubjectMapping[subject], "- Subject:", subject.replace("dbr:","")) | ||
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| print("\nCOMPARISON OF ALGS WHEN BOTH PREDICTED INCORRECTLY") | ||
| #Comparison of algorithms for when both predicted incorrectly | ||
| for subject in bothIncorrect: | ||
| #Alg1 Analysis | ||
| alg1CompSegment = alg1[alg1['sub'] == subject] | ||
| alg1Sample = 0 | ||
| while alg1CompSegment.iloc[alg1Sample,classColLocation] != 1: | ||
| alg1Sample = alg1Sample + 1 | ||
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| #Alg2 Analysis | ||
| alg2CompSegment = alg2[alg2['sub'] == subject] | ||
| alg2Sample = 0 | ||
| while alg2CompSegment.iloc[alg2Sample,classColLocation] != 1: | ||
| alg2Sample = alg2Sample + 1 | ||
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| if alg1Sample > alg2Sample: | ||
| print("Alg1 < Alg2 for relation:", "ID:", idSubjectMapping[subject], "- Subject:", subject.repalce("dbr:","")) | ||
| elif alg1Sample < alg2Sample: | ||
| print("Alg1 > Alg2 for relation:", "ID:", idSubjectMapping[subject], "- Subject:", subject.replace("dbr:","")) | ||
| elif alg1Sample == alg2Sample: | ||
| #Same prediction level, so must compare ratios between highest weight prediction and this wrong preiction | ||
| alg1Ratio = alg1CompSegment.iloc[0,scoreColLocation]/alg1CompSegment.iloc[alg1Sample,scoreColLocation] | ||
| alg2Ratio = alg2CompSegment.iloc[0,scoreColLocation]/alg2CompSegment.iloc[alg2Sample,scoreColLocation] | ||
| #The bigger the ratio the worse the prediction: i.e. 0.5 (first), 0.3, 0.001, 0.0001 (our prediction) vs. | ||
| #0.5 (first), 0.2 (our prediction) | ||
| if alg1Ratio > alg2Ratio: | ||
| print("Alg1 < Alg2 for relation:", "ID:", idSubjectMapping[subject], "- Subject:", subject.repalce("dbr:","")) | ||
| elif alg1Ratio < alg2Ratio: | ||
| print("Alg1 > Alg2 for relation:", "ID:", idSubjectMapping[subject], "- Subject:", subject.replace("dbr:","")) | ||
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| print("\n\nALGORITHM 1: CALCULATING CONFUSION METRICS I.E. TRUE POSITIVE, FALSE POSITIVE, ETC...\n\n") | ||
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| for sample in range(0, alg1.shape[0]): | ||
| if sample % alg1DistinctObjNum == 0: | ||
| if alg1.iloc[sample, classColLocation] == 1: | ||
| print("SID:", alg1.iloc[sample, idColLocation], "- SUBJECT:", alg1.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg1.iloc[sample, objectIDColLocation], "- OBJECT:", alg1.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "TP") | ||
| else: | ||
| print("SID:", alg1.iloc[sample, idColLocation], "- SUBJECT:", alg1.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg1.iloc[sample, objectIDColLocation], "- OBJECT:", alg1.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "FP") | ||
| else: | ||
| if alg1.iloc[sample, classColLocation] == 1: | ||
| print("SID:", alg1.iloc[sample, idColLocation], "- SUBJECT:", alg1.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg1.iloc[sample, objectIDColLocation], "- OBJECT:", alg1.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "FN") | ||
| else: | ||
| print("SID:", alg1.iloc[sample, idColLocation], "- SUBJECT:", alg1.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg1.iloc[sample, objectIDColLocation], "- OBJECT:", alg1.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "TN") | ||
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| print("\n\nALGORITHM 2: CALCULATING CONFUSION METRICS I.E. TRUE POSITIVE, FALSE POSITIVE, ETC...\n\n") | ||
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| for sample in range(0, alg2.shape[0]): | ||
| if sample % alg2DistinctObjNum == 0: | ||
| if alg2.iloc[sample, classColLocation] == 1: | ||
| print("SID:", alg2.iloc[sample, idColLocation], "- SUBJECT:", alg2.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg2.iloc[sample, objectIDColLocation], "- OBJECT:", alg2.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "TP") | ||
| else: | ||
| print("SID:", alg2.iloc[sample, idColLocation], "- SUBJECT:", alg2.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg2.iloc[sample, objectIDColLocation], "- OBJECT:", alg2.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "FP") | ||
| else: | ||
| if alg2.iloc[sample, classColLocation] == 1: | ||
| print("SID:", alg2.iloc[sample, idColLocation], "- SUBJECT:", alg2.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg2.iloc[sample, objectIDColLocation], "- OBJECT:", alg2.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "FN") | ||
| else: | ||
| print("SID:", alg2.iloc[sample, idColLocation], "- SUBJECT:", alg2.iloc[sample, subjectColLocation].replace("dbr:",""), "- OID:", alg2.iloc[sample, objectIDColLocation], "- OBJECT:", alg2.iloc[sample, objectColLocation].replace("dbr:",""), "- CONFUSION:", "TN") | ||
| print("Done.") | ||
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| #WRITING THE RESULTS TO FILES | ||
| else: | ||
| try: | ||
| fileComp = open(outputcomparison,'w') | ||
| except: | ||
| print("Error writing to the specified outputcomparison file, please check -oc argument", file=sys.stderr) | ||
| sys.exit(1) | ||
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| #Printing Results (comparisonWrite function used for this) | ||
| def comparisonWrite(algorithm): | ||
| for subject, score in algorithm.items(): | ||
| fileComp.write("ID: " + str(idSubjectMapping[subject]) + " - Subject: " + str(subject.replace("dbr:","")) + " with score " + str(score) + "\n") | ||
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| fileComp.write("\nALG1 CORRECTLY PREDICTED THE FOLLOWING\n") | ||
| comparisonWrite(correctPredAlg1) | ||
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| fileComp.write("\nALG1 INCORRECTLY PREDICTED THE FOLLOWING\n") | ||
| comparisonWrite(incorrectPredAlg1) | ||
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| fileComp.write("\nALG2 CORRECTLY PREDICTED THE FOLLOWING\n") | ||
| comparisonWrite(correctPredAlg2) | ||
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| fileComp.write("\nALG2 INCORRECTLY PREDICTED THE FOLLOWING\n") | ||
| comparisonWrite(incorrectPredAlg2) | ||
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| bothCorrect = set(correctPredAlg1.keys()) & set(correctPredAlg2.keys()) | ||
| bothIncorrect = set(incorrectPredAlg1.keys()) & set(incorrectPredAlg2.keys()) | ||
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| alg1Correctalg2Incorrect = set(correctPredAlg1.keys()) & set(incorrectPredAlg2.keys()) | ||
| alg2Correctalg1Incorrect = set(correctPredAlg2.keys()) & set(incorrectPredAlg1.keys()) | ||
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| fileComp.write("\nINSTANCES WHERE ALG1 PREDICTED CORRECTLY BUT ALG2 DIDN'T\n") | ||
| for instance in alg1Correctalg2Incorrect: | ||
| fileComp.write("ID: " + str(idSubjectMapping[instance]) + " - Subject: " + str(instance.replace("dbr:","")) + "\n") | ||
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| fileComp.write("\nINSTANCES WHERE ALG2 PREDICTED CORRECTLY BUT ALG1 DIDN'T\n") | ||
| for instance in alg2Correctalg1Incorrect: | ||
| fileComp.write("ID: " + str(idSubjectMapping[instance]) + " - Subject: " + str(instance.replace("dbr:","")) + "\n") | ||
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| #Comparison of algorithms for when both predicted correctly | ||
| fileComp.write("\nCOMPARISON OF ALGS WHEN BOTH PREDICTED CORRECTLY\n") | ||
| for subject in bothCorrect: | ||
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| alg1CompSegment = alg1[alg1['sub'] == subject] | ||
| alg2CompSegment = alg2[alg2['sub'] == subject] | ||
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| #Same prediction level, so must compare ratios between our first correct prediction, and the next prediction | ||
| alg1Ratio = alg1CompSegment.iloc[0,scoreColLocation]/alg1CompSegment.iloc[1,scoreColLocation] | ||
| alg2Ratio = alg2CompSegment.iloc[0,scoreColLocation]/alg2CompSegment.iloc[1,scoreColLocation] | ||
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| #The greater the ratio the better the prediction, i.e. | ||
| #0.5 (our prediction) 0.04 (next prediction) vs. | ||
| #0.5 (our prediction) 0.4 (next prediction) | ||
| if alg1Ratio > alg2Ratio: | ||
| fileComp.write("Alg1 > Alg2 for relation: " + " ID: " + str(idSubjectMapping[subject]) + " - Subject: " + str(subject.replace("dbr:","")) + "\n") | ||
| elif alg1Ratio < alg2Ratio: | ||
| fileComp.write("Alg1 < Alg2 for relation: " + " ID: " + str(idSubjectMapping[subject]) + " - Subject: " + str(subject.replace("dbr:","")) + "\n") | ||
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| fileComp.write("\nCOMPARISON OF ALGS WHEN BOTH PREDICTED INCORRECTLY\n") | ||
| #Comparison of algorithms for when both predicted incorrectly | ||
| for subject in bothIncorrect: | ||
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| #Alg1 Analysis | ||
| alg1CompSegment = alg1[alg1['sub'] == subject] | ||
| alg1Sample = 0 | ||
| while alg1CompSegment.iloc[alg1Sample,classColLocation] != 1: | ||
| alg1Sample = alg1Sample + 1 | ||
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| #Alg2 Analysis | ||
| alg2CompSegment = alg2[alg2['sub'] == subject] | ||
| alg2Sample = 0 | ||
| while alg2CompSegment.iloc[alg2Sample,classColLocation] != 1: | ||
| alg2Sample = alg2Sample + 1 | ||
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| if alg1Sample > alg2Sample: | ||
| fileComp.write("Alg1 < Alg2 for relation: " + " ID: " + str(idSubjectMapping[subject]) + " - Subject: " + str(subject.replace("dbr:","")) + "\n") | ||
| elif alg1Sample < alg2Sample: | ||
| fileComp.write("Alg1 > Alg2 for relation: " + " ID: " + str(idSubjectMapping[subject]) + " - Subject: " + str(subject.replace("dbr:","")) + "\n") | ||
| elif alg1Sample == alg2Sample: | ||
| #Same prediction level, so must compare ratios between highest weight prediction and this wrong preiction | ||
| alg1Ratio = alg1CompSegment.iloc[0,scoreColLocation]/alg1CompSegment.iloc[alg1Sample,scoreColLocation] | ||
| alg2Ratio = alg2CompSegment.iloc[0,scoreColLocation]/alg2CompSegment.iloc[alg2Sample,scoreColLocation] | ||
| #The bigger the ratio the worse the prediction: i.e. 0.5 (first), 0.3, 0.001, 0.0001 (our prediction) vs. | ||
| #0.5 (first), 0.2 (our prediction) | ||
| if alg1Ratio > alg2Ratio: | ||
| fileComp.write("Alg1 < Alg2 for relation: " + " ID: " + str(idSubjectMapping[subject]) + " - Subject: " + str(subject.replace("dbr:","")) + "\n") | ||
| elif alg1Ratio < alg2Ratio: | ||
| fileComp.write("Alg1 > Alg2 for relation: " + " ID: " + str(idSubjectMapping[subject]) + " - Subject: " + str(subject.replace("dbr:","")) + "\n") | ||
| fileComp.close | ||
|
There was a problem hiding this comment. Changing all "missing function calls" you mentioned except this one, because this requires a different output format. |
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| try: | ||
| fileConfAlg1 = open(alg1confusion,"w") | ||
| except: | ||
| print("Error writing to the specified alg1confusion file, please check -oa1 argument", file=sys.stderr) | ||
| sys.exit(1) | ||
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| fileConfAlg1.write("sid,sub,oid,obj,conf\n") | ||
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| for sample in range(0, alg1.shape[0]): | ||
| if sample % alg1DistinctObjNum == 0: | ||
| if alg1.iloc[sample, classColLocation] == 1: | ||
| fileConfAlg1.write(str(alg1.iloc[sample, idColLocation]) + "," + str(alg1.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg1.iloc[sample, objectIDColLocation]) + "," + str(alg1.iloc[sample, objectColLocation].replace("dbr:","")) + ",TP" + "\n") | ||
| else: | ||
| fileConfAlg1.write(str(alg1.iloc[sample, idColLocation]) + "," + str(alg1.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg1.iloc[sample, objectIDColLocation]) + "," + str(alg1.iloc[sample, objectColLocation].replace("dbr:","")) + ",FP" + "\n") | ||
| else: | ||
| if alg1.iloc[sample, classColLocation] == 1: | ||
| fileConfAlg1.write(str(alg1.iloc[sample, idColLocation]) + "," + str(alg1.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg1.iloc[sample, objectIDColLocation]) + "," + str(alg1.iloc[sample, objectColLocation].replace("dbr:","")) + ",FN" + "\n") | ||
| else: | ||
| fileConfAlg1.write(str(alg1.iloc[sample, idColLocation]) + "," + str(alg1.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg1.iloc[sample, objectIDColLocation]) + "," + str(alg1.iloc[sample, objectColLocation].replace("dbr:","")) + ",TN" + "\n") | ||
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| fileConfAlg1.close | ||
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There was a problem hiding this comment. Changed the fileConfAlg1.write and fileConfAlg2.write procedures to call a function which can write both. In many cases it is possible to include functions; however, we are only repeating an event once or twice, and in my opinion there is no need to further abstract code if we call the block only a few times (i.e. 1-2) but if we call code 3+ times then yes it's a good idea to write a function. Let me know if you agree with this. |
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| try: | ||
| fileConfAlg2 = open(alg2confusion,"w") | ||
| except: | ||
| print("Error writing to the specified alg2confusion file, please check -oa2 argument", file=sys.stderr) | ||
| sys.exit(1) | ||
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| fileConfAlg2.write("sid,sub,oid,obj,conf\n") | ||
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| for sample in range(0, alg2.shape[0]): | ||
| if sample % alg2DistinctObjNum == 0: | ||
| if alg2.iloc[sample, classColLocation] == 1: | ||
| fileConfAlg2.write(str(alg2.iloc[sample, idColLocation]) + "," + str(alg2.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg2.iloc[sample, objectIDColLocation]) + "," + str(alg2.iloc[sample, objectColLocation].replace("dbr:","")) + ",TP" + "\n") | ||
| else: | ||
| fileConfAlg2.write(str(alg2.iloc[sample, idColLocation]) + "," + str(alg2.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg2.iloc[sample, objectIDColLocation]) + "," + str(alg2.iloc[sample, objectColLocation].replace("dbr:","")) + ",FP" + "\n") | ||
| else: | ||
| if alg2.iloc[sample, classColLocation] == 1: | ||
| fileConfAlg2.write(str(alg2.iloc[sample, idColLocation]) + "," + str(alg2.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg2.iloc[sample, objectIDColLocation]) + "," + str(alg2.iloc[sample, objectColLocation].replace("dbr:","")) + ",FN" + "\n") | ||
| else: | ||
| fileConfAlg2.write(str(alg2.iloc[sample, idColLocation]) + "," + str(alg2.iloc[sample, subjectColLocation].replace("dbr:","")) + "," + str(alg2.iloc[sample, objectIDColLocation]) + "," + str(alg2.iloc[sample, objectColLocation].replace("dbr:","")) + ",TN" + "\n") | ||
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| fileConfAlg2.close | ||
|
There was a problem hiding this comment. Are all your "Missing function call?" comments regarding code-structure abstraction i.e. turn each stand-by-itself block under a module function and call that function from main? Or did you mean something else? |
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| print("Done, please check output files.") | ||
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| if __name__ == "__main__": | ||
| main() | ||
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You can just pass
add_argument("alg1file", type=str...)and that will become a positional argument. Positional arguments are required. Also, I recommend using more descriptive names for the user, e.g.input-file-1; if you still want the destination to be calledalg1fileyou may passdest="alg1file"so that you don't need to change the rest of your code.