Organize old files

workflow/.old/apps/r/ScriptTemplates/Concatenate_GTF_results.py

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+#!/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 sys, os, string, glob
+
+
+# return the file list
+def list_all_files(Path):
+    list_all_files = []
+    list_all_files = glob.glob(Path +'/*.txt.tsv')
+    return list_all_files
+
+
+# Main function
+
+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)
+
+# Open the output file
+
+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_all_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()
+print("local Process copy of Concatenate_GTF_results.py")