demo

get_mess_from_gff.py

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+
+import sys
+import Make_Transcript_Class
+
+fr_gff_file_in = "temp.gff"
+
+transcript_mess_dir = {}
+
+
+with open(fr_gff_file_in, 'r') as fr_gff_file:
+    for i in fr_gff_file:
+        if i.startswith('#'):
+            continue
+        else:
+            items = i.strip().split('\t')
+            if items[2] == "gene":
+                gene_id = items[-1].split(';')[0].split("ID=")[1]
+            elif items[2] == "mRNA":
+                transcript_id = items[-1].split(';')[0].split("ID=")[1]
+                transcript_mess_dir[transcript_id] = Make_Transcript_Class.Make_Transcript_Class(items[6], gene_id, transcript_id)
+            elif items[2] == "five_prime_UTR":
+                five_prime_UTR_start_site = int(items[3])
+                five_prime_UTR_end_site = int(items[4])
+                five_prime_UTR_mess = (five_prime_UTR_start_site, five_prime_UTR_end_site)
+                transcript_mess_dir[transcript_id].UTR_mess.append(five_prime_UTR_mess)
+            elif items[2] == "exon":
+                exon_start_site = int(items[3])
+                exon_end_site = int(items[4])
+                exon_mess = (exon_start_site, exon_end_site)
+                transcript_mess_dir[transcript_id].exon_mess.append(exon_mess)
+            elif items[2] == "three_prime_UTR":
+                three_prime_UTR_start_site = int(items[3])
+                three_prime_UTR_end_site = int(items[4])
+                three_prime_UTR_mess = (three_prime_UTR_start_site, three_prime_UTR_end_site)
+                transcript_mess_dir[transcript_id].UTR_mess.append(three_prime_UTR_mess)
+            elif items[2] == "CDS":
+                CDS_start_site = int(items[3])
+                CDS_end_site = int(items[4])
+                CDS_mess = (CDS_start_site, CDS_end_site)
+                transcript_mess_dir[transcript_id].CDS_mess.append(CDS_mess)
+
+
+print(len(transcript_mess_dir))
+print(transcript_mess_dir["BMSK10000080.1"].transcript_id)
+print(len(transcript_mess_dir["BMSK10000080.1"].exon_mess))