--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/intelligenetics_io.py	Mon Jan 16 07:03:36 2012 -0500
@@ -0,0 +1,203 @@
+#!/usr/bin/env python
+ 
+#  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 and write sequence information in IntelliGenetics format.
+    
+A sequence file in IG format can contain several sequences, each consisting of a
+number of comment lines that must begin with a semicolon (";"), a line with the 
+sequence name and the sequence itself terminated with the termination character 
+'1' for linear or '2' for circular sequences. The termination caracter is
+defacto optional.
+
+--- Example IG File ---
+
+;H.sapiens fau mRNA, 518 bases
+HSFAU
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
+actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
+gttcagtcaaaaaaaaaa1
+;H.sapiens fau 1 gene, 2016 bases
+HSFAU1
+ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
+gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
+gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
+tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
+accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
+ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2
+
+"""
+
+from corebio.utils import *
+from corebio.seq import *
+from corebio.seq_io import *
+
+
+names = ( 'intelligenetics', 'ig', 'stanford', )
+extensions = ('ig') 
+
+
+example = """
+;H.sapiens fau mRNA, 518 bases
+HSFAU
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
+actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
+gttcagtcaaaaaaaaaa1
+;H.sapiens fau 1 gene, 2016 bases
+HSFAU1
+ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
+gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
+gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
+tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
+accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
+ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2
+"""    
+
+
+
+
+def read(fin, alphabet=None): 
+    """Read and parse an IG file. 
+
+    Args:
+        fin -- A stream or file to read
+        alphabet -- The expected alphabet of the data, if given
+    Returns: 
+        SeqList -- A list of sequences
+    Raises: 
+        ValueError -- If the file is unparsable
+    """         
+    seqs = [ s for s in iterseq(fin, alphabet)]
+    return SeqList(seqs)
+
+    
+def iterseq(fin, alphabet=None):
+    """ Parse an IG file and generate sequences.
+    
+    Args:
+        fin -- A stream or file to read
+        alphabet -- The expected alphabet of the data, if given    
+    Yeilds: 
+        Seq -- One alphabetic sequence at a time.
+    Raises: 
+        ValueError -- If the file is unparsable
+    """
+    alphabet = Alphabet(alphabet)
+
+    seqs = []
+    header = []   
+    start_lineno = -1
+    name = None
+    
+    def build_seq(seqs,alphabet, name, comments, lineno) :
+        try :
+            desc = '\n'.join(comments)
+            s = Seq( "".join(seqs), alphabet, name=name, description=desc)
+        except ValueError :
+             raise ValueError(
+                "Parsed failed with sequence starting at line %d: "
+                "Character not in alphabet: %s" % (lineno, alphabet) )
+        return s
+
+    for lineno, line in enumerate(fin) :
+        line = line.strip()
+        if line == '' : continue
+        if line.startswith(';') :
+            if seqs :
+                # end of sequence
+                yield  build_seq(seqs,alphabet, name, header, start_lineno)
+                header = []
+                seqs = []
+                name = None
+            header.append(line[1:])
+            start_lineno = lineno
+        elif not name :  
+            name = line
+        elif line[-1] == '1' or line[-1]=='2': 
+            # End of sequence
+            seqs.append(remove_whitespace(line[0:-1]))
+            yield  build_seq(seqs,alphabet, name, header, start_lineno)
+            header = []
+            seqs = []       
+            name = None
+        else:
+            seqs.append( remove_whitespace(line))    
+    
+    if seqs :
+        yield build_seq(seqs,alphabet, name, header, start_lineno)
+    return
+    
+    
+    
+
+
+def write(fout, seqs): 
+    """Write an IG file. 
+
+    Args:
+        fout -- A writable stream.
+        seqs  -- A list of Seq's
+    Raises:
+        ValueError -- If a sequence is missing a name
+    """        
+    for s in seqs :
+        writeseq(fout, s)
+
+    
+def writeseq(fout, seq):
+    """ Write a single sequence in IG format.
+
+    Args:
+        afile -- A writable stream.
+        seq  -- A Seq instance
+    Raises:
+        ValueError -- If a sequence is missing a name        
+    """
+
+    desc = seq.description or ''
+    
+    # We prepend ';' to each line
+    for h in desc.splitlines()  :
+        print >> fout, ';' +h
+
+    if not seq.name :
+        raise ValueError(
+            "Write failed with missing sequence name: %s"% str(seq) )
+    print >>fout, seq.name
+    L = len(seq) 
+    line_length = 80
+    for n in range (1+ int(L/line_length)) :
+        print >>fout, seq[n * line_length: (n+1) * line_length] 
+    print >>fout
+    
+    
+    
+    
+     
+
+
+    
+    
+    
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