output on convert

Former-commit-id: 5e24687487a3cbfb3238642fe80ac9e249174c61

Author: bbengfort

apps/convert_fasta.py

@@ -10,6 +10,7 @@
 import os
 import sys
 import shutil
+import brisera
 import tempfile
 
 from brisera.convert import FastaChunker
@@ -48,3 +49,8 @@
     shutil.rmtree(tempdir)
 
     assert not os.path.exists(tempdir)
+
+    print "Processed %i sequences into %i chunks" % (chunker.sequences, chunker.chunks)
+    print "Minimum sequence length: %i" % chunker.min_sequence_len
+    print "Maximum sequence length: %i" % chunker.max_sequence_len
+    print "Saved as Brisera version %s sequence format" % brisera.__version__

brisera/convert.py

@@ -14,6 +14,7 @@ def __init__(self, path):
         self.min_sequence_len = None
         self.max_sequence_len = None
         self.sequences = 0
+        self.chunks    = 0
 
     def chunk(self, sequence):
         """
@@ -45,6 +46,7 @@ def chunk(self, sequence):
             end = min(offset+settings.max_chunk, length)
 
             chunk = sequence[offset:end]
+            self.chunks += 1
             yield (chunk, offset, end == length)
 
             if end == length: