diff swalign.py @ 4:af383638de66 draft

planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/swalign.py	Mon Nov 23 18:44:23 2015 -0500
@@ -0,0 +1,57 @@
+import os
+import ctypes
+
+script_dir = os.path.dirname(os.path.realpath(__file__))
+swalign = ctypes.cdll.LoadLibrary(os.path.join(script_dir, 'swalignc.so'))
+
+
+# C struct for ctypes
+class SeqPairC(ctypes.Structure):
+  _fields_ = [
+    ('a', ctypes.c_char_p),
+    ('alen', ctypes.c_uint),
+    ('b', ctypes.c_char_p),
+    ('blen', ctypes.c_uint),
+  ]
+
+
+# C struct for ctypes
+class AlignC(ctypes.Structure):
+  _fields_ = [
+    ('seqs', ctypes.POINTER(SeqPairC)),
+    ('start_a', ctypes.c_int),
+    ('start_b', ctypes.c_int),
+    ('end_a', ctypes.c_int),
+    ('end_b', ctypes.c_int),
+    ('matches', ctypes.c_int),
+    ('score', ctypes.c_double),
+  ]
+
+
+# The Python version
+class Align(object):
+  def __init__(self, align_c):
+    self.target = align_c.seqs.contents.a
+    self.query = align_c.seqs.contents.b
+    self.start_target = align_c.start_a
+    self.start_query = align_c.start_b
+    self.end_target = align_c.end_a
+    self.end_query = align_c.end_b
+    self.matches = align_c.matches
+    self.score = align_c.score
+
+
+# Initialize functions (define types).
+swalign.smith_waterman.restype = ctypes.POINTER(AlignC)
+swalign.revcomp.restype = ctypes.c_char_p
+
+
+def smith_waterman(target, query):
+  seq_pair = SeqPairC(target, len(target), query, len(query))
+  align_c = swalign.smith_waterman(ctypes.pointer(seq_pair), 1).contents
+  return Align(align_c)
+
+
+def revcomp(seq):
+  """WARNING: This will alter the input string in-place!"""
+  swalign.revcomp(seq)