Merge pull request #49 from loosolab/gtf_creation

Gtf creation
loosolab · Jan 10, 2019 · 13a610f · 13a610f
2 parents 9ab7116 + 8d1ff19
commit 13a610f
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Showing 3 changed files with 18 additions and 14 deletions.
diff --git a/.gitignore b/.gitignore
@@ -203,6 +203,4 @@ venv.bak/
 
 # mypy
 .mypy_cache/
-
-Würde bin/3.1_create_gtf/data/ löschen
-Würde data/ löschen
+/bin/3.1_create_gtf/data/
diff --git a/bin/3.1_create_gtf/Modules/ucsc/ucsc.py b/bin/3.1_create_gtf/Modules/ucsc/ucsc.py
@@ -58,17 +58,21 @@ def read_gff_to_gtf(self):
         with open(self.output, 'r') as csvfile:
             tsvreader = csv.reader(csvfile, delimiter='\t')
             for row in tsvreader:
-                sequence = []
-                sequence.append(row[0])
-                sequence.append("UCSC")
-                sequence.append(row[3].lower().replace(' ', '_'))
-                sequence.append(row[1])
-                sequence.append(row[2])
-                sequence.append(".")
-                sequence.append(row[5])
-                sequence.append(".")
-                sequence.append('; '.join([self.find_ID(''.join(row[11:])), 'activity \"'+", ".join(self.get_activity(''.join(row[11:]))) + '"'])+";")
-                gtf_lines.append(sequence)
+                if row[9] not in ["region", "sequence_feature",
+                                  "CAAT_signal", "stem_loop",
+                                  "sequence_secondary_structure"]:
+
+                    sequence = []
+                    sequence.append(row[0])
+                    sequence.append("UCSC")
+                    sequence.append(row[9].lower().replace(' ', '_'))
+                    sequence.append(row[1])
+                    sequence.append(row[2])
+                    sequence.append(".")
+                    sequence.append(row[5])
+                    sequence.append(".")
+                    sequence.append('; '.join([self.find_ID(''.join(row[11:])), 'activity \"'+", ".join(self.get_activity(''.join(row[11:]))) + '"'])+";")
+                    gtf_lines.append(sequence)
 
             return gtf_lines
 

diff --git a/bin/3.1_create_gtf/RegGTFExtractor.py b/bin/3.1_create_gtf/RegGTFExtractor.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 """
 
 RegGTFExtractor.py extracts regulatory-data from Ensembl and UCSC databases