131 lines
4.8 KiB
Python
131 lines
4.8 KiB
Python
#!/usr/bin/env python
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"""
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Improved code to determine the origin column (OligCol) without user input of the argument
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and removed the former sys.argv[2]. JWR 22_0816
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"""
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"""
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this code can be used for the parse of the REMc "-finalTable.csv" output file
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to make a series of subdatasets, which reflect the pedigree structure
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of the way cluters breaking up.
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"""
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import sys, os, string, glob
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try:
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data_file_Path = sys.argv[1]
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#print data_file_Path
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#cluster_ori_col_num = sys.argv[2]
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output_path = sys.argv[2]
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except:
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print ('Usage: python parse_clustering_result_to_Pedigree_Dataset_and_genelist.py /datasetPath/datasetfilename cluster_origin_column_num output_path_name')
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print ('Data file not found')
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sys.exit(1)
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#define a function to reading files and generate the list
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def read_file(file_path):
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with open(file_path, 'r') as file:
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attributes = file.readline().strip().split(',')
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gene_list = [elements[1] for line in file for elements in [line.strip().split(',')]]
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return gene_list
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# define a function to write the list into a file named in hierarchical series
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def write_cluster_orf_list(orf_list, output_dir, cluster_name):
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cluster_file_path = os.path.join(output_dir, f"cluster_name, 'txt')
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with open(cluster_file_path, 'w') as outfile:
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for orf in orf_list:
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outfile.write(orf.strip() + '\n')
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# define a function to write the clusters information into a series of files
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def write_cluster_results(attributes, orf_list, data_dict, output_directory, cluster_name):
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file_path = os.path.join(output_directory, f"{cluster_name}-finaltable.csv")
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with open(file_path, 'w') as output_file:
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output_file.write(attributes)
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output_file.write('\n')
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for orf in orf_list:
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output_file.write(data_dict[orf.strip()].strip())
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output_file.write('\n')
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# define a function to write the cluster name origina extensive final table
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def write_extended_final_table(attributes, data, ori_name_column_number, output_directory, output_file_name):
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output_file_path = os.path.join(output_directory, f"{output_file_name}-oriExtFinalTable.csv")
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with open(output_file_path, 'w') as output_file:
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output_file.write(attributes)
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output_file.write('\n')
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for orf in data:
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elements = data[orf].split(',')
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ori_name_list = elements[int(ori_name_column_number)-1].strip().split(';')
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for ori_name in ori_name_list:
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elements.append(orii_name.strip())
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output_file.write(','.join(elements))
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output_file.write('\n')
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# Read the data file
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try:
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data = open(data_file_Path,'r')
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except OSError:
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print ('input file does not exists')
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# first the title line would be read and kept
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attributes = data.readline().strip().split(',')
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print(attributes)
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print(len(attributes))
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OrigCol= len(attributes) - 1
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print(OrigCol)
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# then the data
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data_dict = {}
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for data_line in data:
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data_line = data_line.strip()
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line_elements = data_line.split(',')
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orf_identifier = line_elements[1].strip().upper()
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data_dict[orf_identifier] = ','.join(line_elements).upper()
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data.close()
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#print dataDic
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print ("OrigCol is ", str(OrigCol))
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fileDic = {}
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for orf in dataDic:
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line = dataDic[orf].split(',')
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#read the cluster name len(attributes)
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clusterOrigin = line[int(OrigCol) - 1]
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#clusterOrigin = line[int(cluster_ori_col_num) - 1]
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#print clusterOrigin
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clusterOrigin = clusterOrigin.strip()
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#print clusterOrigin
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clusterIdentifier = clusterOrigin.split(';')[0:-1]
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#print clusterIdentifier
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for identifier in clusterIdentifier:
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identifier = identifier.strip()
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upper_identifier = identifier.upper()
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if upper_identifier not in fileDic:
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fileDic[upper_identifier] = line[1]
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else:
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fileDic[upper_identifier] += ',' + line[1]
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input_file_identifier = data_file_Path.strip().split('/')[-1].strip().split('.csv')[-3]
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#make the output folder
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try:
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os.mkdir(str(output_path)+str(input_file_identifier))
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except OSError:
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print ('dir exists')
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#Writing the extensive ori name finaltable
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Writing_ext_final_table(attributeLine, dataDic,str(OrigCol),str(output_path)+str(input_file_identifier), str(input_file_identifier))
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#Writing_ext_final_table(attributeLine, dataDic,cluster_ori_col_num,str(output_path)+str(input_file_identifier), str(input_file_identifier))
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#write the genelist files
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for cluster_name in fileDic:
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#print fileDic[cluster_name].split(',')
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Writing_clusterORF_list(fileDic[cluster_name].split(','), str(output_path)+str(input_file_identifier), cluster_name)
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#write the cluster result files
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Writing_cluster_results(attributeLine, fileDic[cluster_name].split(','), dataDic,str(output_path)+str(input_file_identifier),cluster_name)
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