--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/stockholm_io.py	Fri Jan 13 07:18:19 2012 -0500
@@ -0,0 +1,172 @@
+ 
+#  Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
+#
+#  This software is distributed under the MIT Open Source License.
+#  <http://www.opensource.org/licenses/mit-license.html>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a 
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+#  THE SOFTWARE.
+#
+
+"""Read a multiple sequence alignment in STOCKHOLM format.
+
+This file format is used by PFAM and HMMER. At present, all annotation
+information is ignored.
+
+See: 
+    - http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html
+    - HMMER manual
+
+"""
+
+import re
+
+from corebio.utils import *
+from corebio.seq import *
+from corebio.seq_io import *
+
+
+
+example = """
+# STOCKHOLM 1.0
+#=GF ID CBS
+#=GF AC PF00571
+#=GF DE CBS domain
+#=GF AU Bateman A
+#=GF CC CBS domains are small intracellular modules mostly found  
+#=GF CC in 2 or four copies within a protein. 
+#=GF SQ 67
+#=GS O31698/18-71 AC O31698
+#=GS O83071/192-246 AC O83071
+#=GS O83071/259-312 AC O83071
+#=GS O31698/88-139 AC O31698
+#=GS O31698/88-139 OS Bacillus subtilis
+O83071/192-246          MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS
+#=GR O83071/192-246 SA  999887756453524252..55152525....36463774777
+O83071/259-312          MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY
+#=GR O83071/259-312 SS  CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE
+O31698/18-71            MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS
+#=GR O31698/18-71 SS    CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH
+O31698/88-139           EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
+#=GR O31698/88-139 SS   CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH
+#=GC SS_cons            CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH
+O31699/88-139           EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
+#=GR O31699/88-139 AS   ________________*__________________________
+#=GR_O31699/88-139_IN   ____________1______________2__________0____
+//
+"""
+
+
+
+names = ("stockholm", "pfam",)
+extensions = ('sth', 'stockholm', 'align')
+
+
+header_line = re.compile(r'#\s+STOCKHOLM\s+1.\d\s+$')
+
+def iterseq(fin, alphabet=None):
+    """Iterate over the sequences in the file."""
+    # Default implementation
+    return iter(read(fin, alphabet) )
+
+
+def read(fin, alphabet=None) :  
+    alphabet = Alphabet(alphabet)      
+    seq_ids = []
+    seqs = []
+    block_count = 0
+    
+    
+    for token in _scan(fin):
+        if token.typeof== "begin_block":
+            block_count = 0
+        elif token.typeof == "seq_id":
+            if len(seqs) <= block_count :
+                seq_ids.append(token.data)
+                seqs.append([])
+        elif token.typeof == "seq":
+            if not alphabet.alphabetic(token.data) :
+                raise ValueError (
+                    "Character on line: %d not in alphabet: %s : %s" % (
+                    token.lineno, alphabet, token.data) )
+            seqs[block_count].append(token.data)
+            block_count +=1
+
+          
+    seqs = [ Seq("".join(s), alphabet, name= i) for s,i in zip(seqs,seq_ids)]
+    return SeqList(seqs)
+
+
+def _scan( fin ):
+
+    header, body, block = range(3)
+    
+    yield Token("begin")
+    state = header
+    for L, line in enumerate(fin):
+        
+
+        if state==header :
+            if line.isspace() : continue
+            m = header_line.match(line)
+            state = body
+            if m is not None :
+                # print "header: ", m.group() 
+                yield Token("header", m.group() )
+                continue
+            else :
+                 raise ValueError("Parse error on line: %d" % L)
+        
+        
+        if state == body :
+            if line.isspace() : continue
+            yield Token("begin_block")
+            state = block
+            # fall through to block
+        
+        if state ==  block:        
+            if line.isspace() :
+                yield Token("end_block")
+                state = body
+                continue
+            if line.strip() == '//' :
+                yield Token("end_block")
+                return
+            
+            
+            if line[0] =='#' :  # Comment or annotation line 
+                continue
+   
+            name_seq = line.split(None,1) # Split into two parts at first whitespace 
+            if len(name_seq) != 2 : 
+                raise ValueError("Parse error on line: %d" % L)
+ 
+            
+            yield Token("seq_id", name_seq[0].strip() )
+            yield Token("seq", name_seq[1].strip() )
+            continue
+
+        # END state blocks. If I ever get here something has gone terrible wrong
+        raise RuntimeError()
+    
+
+
+
+
+
+