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removed click, added parameter check #1

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removed click, added parameter check #1

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63 changes: 50 additions & 13 deletions CODE/feat_extract/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,21 +27,58 @@
profiler = None

# -r r'.\Chap\train' -s r'.\Chap\test' -rs r'.\Chap' --testFeatures True --trainFeatures True
# -r r'E:\Dropbox\Dropbox\bioInf_lab\AA_info\CODE\feat_extract\Chap\train' -s r'E:\Dropbox\Dropbox\bioInf_lab\AA_info\CODE\feat_extract\Chap\test' -rs r'E:\Dropbox\Dropbox\bioInf_lab\AA_info\CODE\feat_extract\Chap' --testFeatures True --trainFeatures True

# -r r'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\train' -s r'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\test' -rs r'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\results' --testFeatures True --trainFeatures True
# -r 'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\train' -s 'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\test' -rs 'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\results' --testFeatures True --trainFeatures True
# -r 'C:\\Users\\Michael\\Desktop\\Feature_Extract\\test_seq\\Chap\\train' -s 'C:\\Users\\Michael\\Desktop\\Feature_Extract\\test_seq\\Chap\\test' -rs 'C:\\Users\\Michael\\Desktop\\Feature_Extract\\test_seq\\Chap\\results' --testFeatures True --trainFeatures True
# -r C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\train -s C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\test -rs C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\results --testFeatures True --trainFeatures True

##ADD OPT for classifier type , and if to use classifier tuning
@click.command()
@click.option('--trainingSetDir','-r','trainingDir',default=r'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\train',
help='The path to the training set fasta files', type = str)
@click.option('--testingSetDir','-s','testingDir',default=r'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\test',
help='The path to the testing set fasta files', type = str)
@click.option('--resultsDir','-rs','resultsDir',default=r'.\results',
help='The path to directory to write the results files', type = str)
@click.option('--trainFeatures','-rf','GetTrainingFeatures',default=True,help='Whether to extract the training set features', type = bool)
@click.option('--testFeatures','-sf','GetTestFeatures',default=False,help='Whether to get the testing set features', type = bool)
@click.option('--classType','-ct','classType',default='file',help="Defines the classname of each protein, by \'dir\', \'file\', or \'id\'.", type = str)
def pipeline(trainingDir,testingDir,resultsDir, GetTrainingFeatures,GetTestFeatures, classType):
import argparse

parser = argparse.ArgumentParser()
# @click.option('--trainingSetDir','-r','trainingDir',default=r'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\train',
# help='The path to the training set fasta files', type = str)
# @click.option('--testingSetDir','-s','testingDir',default=r'C:\Users\Michael\Desktop\Feature_Extract\test_seq\Chap\test',
# help='The path to the testing set fasta files', type = str)
# @click.option('--resultsDir','-rs','resultsDir',default=r'.\results',
# help='The path to directory to write the results files', type = str)
# @click.option('--trainFeatures','-rf','GetTrainingFeatures',default=True,help='Whether to extract the training set features', type = bool)
# @click.option('--testFeatures','-sf','GetTestFeatures',default=False,help='Whether to get the testing set features', type = bool)
# @click.option('--classType','-ct','classType',default='file',help="Defines the classname of each protein, by \'dir\', \'file\', or \'id\'.", type = str)

parser.add_argument('--trainingSetDir','-r',dest='trainingDir', type = str,help='The path to the training set fasta files')
parser.add_argument('--testingSetDir','-s',dest='testingDir', type = str,help='The path to the testing set fasta files')
parser.add_argument('--resultsDir','-rs',dest='resultsDir', type = str,help='The path to directory to write the results files')
parser.add_argument('--trainFeatures','-rf',dest='GetTrainingFeatures', type = bool,help='Whether to extract the training set features')
parser.add_argument('--testFeatures','-sf',dest='GetTestFeatures', type = bool,help='Whether to get the testing set features')
parser.add_argument('--classType','-ct',dest='classType', type = str,help='Defines the classname of each protein, by \'dir\', \'file\', or \'id\'."')

def pipeline():
results = parser.parse_args()
trainingDir=results.trainingDir
testingDir=results.testingDir
resultsDir=results.resultsDir
GetTrainingFeatures=results.GetTrainingFeatures
GetTestFeatures=results.GetTestFeatures
classType=results.classType
if (not os.path.exists(trainingDir)):
print('training dir doesn\'t exist')
exit()
if (not os.path.exists(testingDir)):
print('testing dir doesn\'t exist')
exit()
if (not os.path.exists(resultsDir)):
print('results dir doesn\'t exist')
exit()
if not (os.access(trainingDir, os.R_OK) and os.access(trainingDir, os.X_OK) and os.access(trainingDir, os.W_OK)):
print('don\' have permission to access training dir')
exit()
if not (os.access(testingDir, os.R_OK) and os.access(testingDir, os.X_OK) and os.access(testingDir, os.W_OK)):
print('don\' have permission to access testing dir')
exit()
if not (os.access(resultsDir, os.R_OK) and os.access(resultsDir, os.X_OK) and os.access(resultsDir, os.W_OK)):
print('don\' have permission to access results dir')
exit()
print(profiler)
# change here to the training data folder
# trainingDir = r'E:\Dropbox\Dropbox\BioInformatics Lab\AA_Information\CODE\Feature_Extract\test_seq\Chap'
Expand Down