Squashed initial commit

qhtcp-workflow/apps/python/dCon.py

@@ -0,0 +1,131 @@
+#!/usr/bin/env python
+"""
+Reads the REMc "-finalTable.csv" output file and makes a series of subdatasets
+that reflect the pedigree structure of the way clusters break up.
+"""
+
+import sys
+import os
+import string
+import glob
+
+
+def reading_single_file(file_path):
+    """
+    Reads a file and generates a list of gene names.
+    """
+    with open(file_path, 'r') as data:
+        attribute_line = data.readline().strip()
+        attributes = attribute_line.split(',')
+
+        gene_list = []
+        for dataline in data:
+            dataline = dataline.strip()
+            elements = dataline.split(',')
+            gene_list.append(elements[1])
+
+    return gene_list
+
+
+def writing_cluster_orf_list(list, output_dir, real_cluster_ori_name):
+    """
+    Writes a list of ORF names into a file in hierarchical series.
+    """
+    outfile_path = os.path.join(output_dir, f"{real_cluster_ori_name}.txt")
+    with open(outfile_path, 'w') as outfile:
+        for orf in list:
+            outfile.write(orf.strip())
+            outfile.write('\n')
+
+
+def writing_cluster_results(attributes, orf_list, dic, output_dir, real_cluster_ori_name):
+    """
+    Writes clusters information into a series of files.
+    """
+    outfile_path = os.path.join(output_dir, f"{real_cluster_ori_name}-finaltable.csv")
+    with open(outfile_path, 'w') as outfile:
+        outfile.write(attributes)
+        outfile.write('\n')
+        for orf in orf_list:
+            outfile.write(dic[orf.strip()].strip())
+            outfile.write('\n')
+
+
+def writing_ext_final_table(attributes, dic, ori_name_col_num, output_dir, output_file_name):
+    """
+    Writes the cluster name extensive final table.
+    """
+    outfile_path = os.path.join(output_dir, f"{output_file_name}-oriExtFinalTable.csv")
+    with open(outfile_path, 'w') as outfile:
+        outfile.write(attributes)
+        outfile.write('\n')
+        for orf in dic:
+            elements = dic[orf].split(',')
+            ori_name_list = elements[int(ori_name_col_num) - 1].strip().split(';')
+            for ori_name in ori_name_list:
+                elements.append(ori_name.strip())
+            outfile.write(','.join(elements))
+            outfile.write('\n')
+
+
+def main():
+    """
+    Main function to parse the REMc -finalTable.csv output file.
+    """
+    try:
+        data_file_path = sys.argv[1]
+        output_path = sys.argv[2]
+    except IndexError:
+        print('Usage: python parse_clustering_result_to_Pedigree_Dataset_and_genelist.py '
+              '/datasetPath/datasetfilename cluster_origin_column_num output_path_name')
+        print('Data file not found')
+        sys.exit(1)
+
+    try:
+        with open(data_file_path, 'r') as data:
+            attribute_line = data.readline().strip()
+            attributes = attribute_line.split(',')
+            orig_col = len(attributes) - 1
+
+            data_dict = {}
+            for dataline in data:
+                dataline = dataline.strip()
+                elements = dataline.split(',')
+                data_dict[str.upper(elements[1].strip())] = ','.join(elements).upper()
+
+    except FileNotFoundError:
+        print('Input file does not exist')
+        sys.exit(1)
+
+    file_dict = {}
+    for orf in data_dict:
+        line = data_dict[orf].split(',')
+        cluster_origin = line[int(orig_col) - 1].strip()
+        cluster_identifier = cluster_origin.split(';')[0:-1]
+
+        for i, identifier in enumerate(cluster_identifier):
+            identifier = identifier.strip()
+            if identifier not in file_dict:
+                file_dict[identifier] = line[1]
+            else:
+                file_dict[identifier] = f"{file_dict[identifier]},{line[1]}"
+
+    input_file_identifier = os.path.basename(data_file_path).split('.csv')[0]
+    output_dir = os.path.join(output_path, input_file_identifier)
+    os.makedirs(output_dir, exist_ok=True)
+
+    # Writing the extensive ori name finaltable
+    writing_ext_final_table(attribute_line, data_dict, orig_col, output_dir, input_file_identifier)
+
+    # Writing the genelist files
+    for cluster_name in file_dict:
+        writing_cluster_orf_list(file_dict[cluster_name].split(','), output_dir, cluster_name)
+
+        # Writing the cluster result files
+        writing_cluster_results(attribute_line, file_dict[cluster_name].split(','), data_dict,
+                                output_dir, cluster_name)
+
+
+if __name__ == '__main__':
+    main()
+