--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/fasta_io.py	Thu Oct 27 12:09:09 2011 -0400
@@ -0,0 +1,230 @@
+#!/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 FASTA format.
+    
+This is a very common format for unannotated biological sequence data, 
+accepted by many multiple sequence alignment programs. Each sequence 
+consists of a single-line description, followed by lines of sequence data. 
+The first character of the description line is a greater-than (">") symbol 
+in the first column. The first word of the description is often the name or 
+ID of the sequence. Fasta files containing multiple sequences have one 
+sequence listed right after another. 
+
+
+Example Fasta File ::
+
+>Lamprey GLOBIN V - SEA LAMPREY
+PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL
+TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK
+VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------
+>Hagfish GLOBIN III - ATLANTIC HAGFISH
+PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK
+KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK
+ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA----------
+>Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG
+----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL
+GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT
+VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH-----------
+
+
+"""
+import re
+from corebio.utils import *
+from corebio.seq import *
+from corebio.seq_io import *
+
+
+names = ( 'fasta', 'pearson', 'fa')
+extensions = ('fa', 'fasta', 'fast', 'seq', 'fsa', 'fst', 'nt', 'aa','fna','mpfa', 'faa', 'fnn','mfasta') 
+
+
+example = """
+>Lamprey GLOBIN V - SEA LAMPREY
+PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL
+TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK
+VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------
+
+>Hagfish GLOBIN III - ATLANTIC HAGFISH
+PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK
+KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK
+ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA----------
+
+>Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG
+----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL
+GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT
+VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH-----------
+
+"""    
+
+
+def read(fin, alphabet=None): 
+    """Read and parse a fasta 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)]
+    name = names[0]
+    if hasattr(fin, "name") : name = fin.name    
+    return SeqList(seqs, name=name)
+
+
+def readseq(fin, alphabet=None) :
+    """Read one sequence from the file, starting 
+    from the current file position."""
+    return iterseq(fin, alphabet).next()
+    
+     
+def iterseq(fin, alphabet=None):
+    """ Parse a fasta 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 = []
+    comments = []   # FIXME: comments before first sequence are lost.
+    header = None
+    header_lineno = -1
+    
+    def build_seq(seqs,alphabet, header, header_lineno,comments) :
+        try :
+            name = header.split(' ',1)[0]
+            if comments :
+                header += '\n' + '\n'.join(comments)
+            s = Seq( "".join(seqs), alphabet, name=name, description=header)
+        except ValueError:
+             raise ValueError(
+                "Parsed failed with sequence starting at line %d: "
+                "Character not in alphabet: %s" % (header_lineno, alphabet) )
+        return s
+
+    for lineno, line in enumerate(fin) :
+        line = line.strip()
+        if line == '' : continue
+        if line.startswith('>') :
+            if header is not None :
+                yield  build_seq(seqs,alphabet, header, header_lineno, comments)
+                header = None
+                seqs = []
+            header = line[1:]
+            header_lineno = lineno
+            comments = []
+        elif line.startswith(';') : 
+            # Optional (and unusual) comment line
+            comments.append(line[1:])           
+        else :
+            if header is None :
+                raise ValueError (
+                    "Parse failed on line %d: sequence before header"  
+                    % (lineno) )
+            seqs.append(line)    
+
+    if not seqs: return
+    yield build_seq(seqs,alphabet, header, header_lineno, comments)
+
+     
+def write(fout, seqs): 
+    """Write a fasta file. 
+
+    Args:
+        fout -- A writable stream.
+        seqs  -- A list of Seq's
+    """ 
+    if seqs.description :
+        for line in seqs.description.splitlines():
+            print >>fout, ';'+ line        
+    for s in seqs :
+        writeseq(fout, s)
+
+    
+def writeseq(afile, seq):
+    """ Write a single sequence in fasta format.
+
+    Args:
+        afile -- A writable stream.
+        seq  -- A Seq instance
+    """
+
+    header = seq.description or seq.name or ''
+    
+    # We prepend '>' to the first header line
+    # Additional lines start with ';' to indicate comment lines
+    if header :
+        header = header.splitlines()  
+        print >>afile, '>'+header[0]
+        if len(header) > 1 :
+            for h in header[1:] :
+                print >>afile, ';' +h
+    else :
+        print >>afile, '>'
+    
+    L = len(seq) 
+    line_length = 80
+    for n in range (1+ L/line_length) :
+        print >>afile, seq[n * line_length: (n+1) * line_length] 
+    print >>afile
+    
+    
+def index(afile, alphabet=None) :
+    """Return a FileIndex for the fasta file. Sequences can be retrieved
+    by item number or name.
+    """
+    def parser( afile) :
+        return readseq(afile, alphabet)
+    
+    key = re.compile(r"^>\s*(\S*)")
+    def linekey( line):
+        k = key.search(line)
+        if k is None : return None
+        return k.group(1)
+        
+    return FileIndex(afile, linekey, parser)
+
+                
+        
+        
+        
+        
+        
+         
+
+
+    
+    
+    
\ No newline at end of file