Squashed initial commit

qhtcp-workflow/apps/python/concatGTFResults.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+# This code is to concatenate the batch GO Term Finder results (.tsv) generated from batch GTF perl code(Chris Johnson, U of Tulsa) into a list table
+
+import os
+import glob
+
+def list_files(directory):
+    """Return a list of all files in the given directory."""
+    return glob.glob(os.path.join(directory, '*.txt.tsv'))
+
+def concatenate_gtf_results(data_dir, output_file):
+    """Concatenate the GTF results into a single file."""
+    output = open(output_file, 'w')
+
+    files = list_files(data_dir)
+    files.sort()
+
+    for file_path in files:
+        file_name = os.path.basename(file_path).rstrip('.txt.tsv')
+        with open(file_path, 'r') as f:
+            labels = f.readline().strip().split('\t')
+            output.write('\t'.join(labels) + '\n')
+
+            for line in f:
+                line = line.strip().strip('\t')
+                if line:
+                    output.write(line + '\n')
+
+    output.close()
+
+if __name__ == '__main__':
+    if len(sys.argv) != 3:
+        print('Usage: python Concatenate_GTF_results.py data_dir output_file')
+        sys.exit(1)
+
+    data_dir = sys.argv[1]
+    output_file = sys.argv[2]
+
+    concatenate_gtf_results(data_dir, output_file)
+
+
+
+
+
+# Old version
+# def list_files(directory):
+#     """Return a list of all files in the given directory."""
+#     return glob.glob(os.path.join(directory, '*.txt.tsv'))
+
+# try:
+#    data_file_Path = sys.argv[1]
+#    output_file_Path = sys.argv[2]
+# except: 
+#    print ('Usage: python Concatenate_GTF_results.py /datasetPath /outputFilePath_and_Name')
+#    print ('Data file not found, error in given directory')
+#    sys.exit(1)
+
+# try:
+#     output = open(output_file_Path, 'w')
+# except OSError:
+#     print ('output file error')
+
+# # get all the GTF result files in given directory
+# File_list = []
+# File_list = list_files(data_file_Path)
+# File_list.sort()
+
+# i = 0
+# for file in File_list:
+#     #parse the file names given in absolute path
+#     file_name = file.strip().split('/')[-1]
+#     file_name = file_name.rstrip('.txt.tsv')
+#     # function to read tsv files from a given directory
+#     #open the file
+#     data = open(file,'r')
+#     #reading the label line
+#     labelLine = data.readline()
+#     label = labelLine.strip().split('\t')
+#     #write the label
+#     #updates2010July26: update following label writing code	
+#     if i == 0:
+#     #    output.write('cluster origin')
+#         for element in label:
+#             output.write(element)
+#             output.write('\t')
+#     i = i + 1
+#     #updates2010July26 End
+#     #switch to the next line
+#     output.write('\n')
+
+#     #read the GO terms
+#     GOTermLines = data.readlines()
+#     for GOTerm in GOTermLines:
+#         GOTerm = GOTerm.strip().strip('\t')
+#         if GOTerm != '':
+# 	    #updates2010July26: remove the code to write the first column 'REMc cluster ID'
+#             #output.write(file_name)
+#             #output.write('\t')
+# 	    ##updates2010July26 update end
+#             output.write(GOTerm + '\n')
+#             #output.write('\n')
+# output.close()
+