diff extract_features.py @ 4:4de31938431b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e

--- a/extract_features.py	Fri May 22 04:55:25 2015 -0400
+++ b/extract_features.py	Fri Oct 20 03:48:57 2017 -0400
@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 
-import os
+import argparse
 import sys
-import argparse
 import textwrap
 
+
 def main( args ):
     """
     Extract the protein and coding section from an augustus gff, gtf file
@@ -45,6 +45,22 @@
             if line.startswith('start gene'):
                 gene_name = line[11:].strip()
 
+            if protein_seq:
+                if line.endswith(']'):
+                    protein_seq += line[:-1]
+                    po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
+                    protein_seq = ''
+                else:
+                    protein_seq += line
+
+            if coding_seq:
+                if line.endswith(']'):
+                    coding_seq += line[:-1]
+                    co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
+                    coding_seq = ''
+                else:
+                    coding_seq += line
+
             if args.protein and line.startswith('protein sequence = ['):
                 if line.endswith(']'):
                     protein_seq = line[20:-1]
@@ -63,26 +79,12 @@
                     line = line[19:]
                     coding_seq = line
 
-            if protein_seq:
-                if line.endswith(']'):
-                    protein_seq += line[:-1]
-                    po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
-                    protein_seq = ''
-                else:
-                    protein_seq += line
-
-            if coding_seq:
-                if line.endswith(']'):
-                    coding_seq += line[:-1]
-                    co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
-                    coding_seq = ''
-                else:
-                    coding_seq += line
     if args.codingseq:
         co.close()
     if args.protein:
         po.close()
 
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser.add_argument('-p', '--protein', help='Path to the protein file.')
@@ -90,4 +92,3 @@
 
     args = parser.parse_args()
     main( args )
-