Updated find_representative_transcripts.py by including GTF writer

scripts/find_representative_transcripts.py

@@ -176,6 +176,29 @@ def get_rep_trans(file_name = "test"):
         rep_transcripts = _re_format(rep_trans)
         return(rep_transcripts )
 
+def gtf_file_writer (original_file, output_file): 
+    """
+    this function writes the output GTF file
+    """
+    output = []
+    rep_transcript_dict = get_rep_trans(original_file)
+
+    with open(original_file, 'r') as f:
+            for entry in f: 
+                if entry[0] != '#':
+                    attributes = attributs_converter(entry)
+                    type_ = attributes[2]
+                    if type_ == 'gene':
+                        gene_id = find_in_attributs(attributes, 'gene_id')
+                        output.append(entry)
+                    if type_ != 'gene':
+                        transcript_id = find_in_attributs(attributes, 'transcript_id')
+                        if rep_transcript_dict[gene_id] == transcript_id:
+                            output.append(entry)
+
+    with open(output_file, 'w') as last_file:
+        last_file.write(output)
+
 def _test(): 
     """
     This funtion is ment to be run for test