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+++ b/corebio/seq_io/__init__.py	Fri Jan 13 07:18:19 2012 -0500
@@ -0,0 +1,261 @@
+
+#  Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
+#  Copyright (c) 2006, The Regents of the University of California, through 
+#  Lawrence Berkeley National Laboratory (subject to receipt of any required
+#  approvals from the U.S. Dept. of Energy).  All rights reserved.
+
+#  This software is distributed under the new BSD Open Source License.
+#  <http://www.opensource.org/licenses/bsd-license.html>
+#
+#  Redistribution and use in source and binary forms, with or without 
+#  modification, are permitted provided that the following conditions are met: 
+#
+#  (1) Redistributions of source code must retain the above copyright notice, 
+#  this list of conditions and the following disclaimer. 
+#
+#  (2) Redistributions in binary form must reproduce the above copyright 
+#  notice, this list of conditions and the following disclaimer in the 
+#  documentation and or other materials provided with the distribution. 
+#
+#  (3) Neither the name of the University of California, Lawrence Berkeley 
+#  National Laboratory, U.S. Dept. of Energy nor the names of its contributors 
+#  may be used to endorse or promote products derived from this software 
+#  without specific prior written permission. 
+#
+#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+#  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+#  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+#  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
+#  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+#  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+#  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+#  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+#  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+#  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+#  POSSIBILITY OF SUCH DAMAGE. 
+
+
+
+
+
+""" Sequence file reading and writing.
+
+Biological sequence data is stored and transmitted using a wide variety of
+different file formats. This package provides convient methods to read and
+write several of these file fomats.
+
+CoreBio is often capable of guessing the correct file type, either from the
+file extension or the structure of the file:
+>>> import corebio.seq_io
+>>> afile = open("test_corebio/data/cap.fa")
+>>> seqs = corebio.seq_io.read(afile)
+
+Alternatively, each sequence file type has a seperate module named FILETYPE_io
+(e.g. fasta_io, clustal_io).
+>>> import corebio.seq_io.fasta_io
+>>> afile = open("test_corebio/data/cap.fa")
+>>> seqs = corebio.seq_io.fasta_io.read( afile )
+
+Sequence data can also be written back to files:
+>>> fout = open("out.fa", "w")
+>>> corebio.seq_io.fasta_io.write( fout, seqs )
+
+
+Supported File Formats
+----------------------
+
+Module              Name            Extension  read write features   
+---------------------------------------------------------------------------
+array_io            array, flatfile             yes  yes    none
+clustal_io          clustalw        aln         yes  yes
+fasta_io            fasta, Pearson  fa          yes  yes    none
+genbank_io          genbank         gb          yes         
+intelligenetics_io  intelligenetics ig          yes  yes
+msf_io              msf             msf         yes
+nbrf_io             nbrf, pir       pir         yes
+nexus_io            nexus           nexus       yes
+phylip_io           phylip          phy         yes
+plain_io            plain, raw      txt         yes  yes    none
+table_io            table           tbl         yes  yes    none
+
+Each IO module defines one or more of the following functions and variables:
+
+read(afile, alphabet=None) 
+    Read a file of sequence data and return a SeqList, a collection
+    of Seq's (Alphabetic strings) and features.
+
+read_seq(afile, alphabet=None)
+    Read a single sequence from a file.
+
+iter_seq(afile, alphabet =None) 
+    Iterate over the sequences in a file. 
+    
+index(afile, alphabet = None)
+    Instead of loading all of the sequences into memory, scan the file and
+    return an index map that will load sequences on demand. Typically not
+    implemented for formats with interleaved sequences.
+
+write(afile, seqlist)
+    Write a collection of sequences to the specifed file.
+
+write_seq(afile, seq)
+    Write one sequence to the file. Only implemented for non-inteleaved, 
+    headerless formats, such as fasta and plain.
+
+example
+    A string containing a short example of the file format
+
+names
+    A list of synonyms for the file format. e.g. for fasta_io, ( 'fasta',    
+    'pearson', 'fa'). The first entry is the preferred format name.
+
+extensions
+    A list of file name extensions used for this file format. e.g. 
+    fasta_io.extensions is ('fa', 'fasta', 'fast', 'seq', 'fsa', 'fst', 'nt',
+    'aa','fna','mpfa').  The preferred or standard extension is first in the 
+    list.
+
+
+Attributes :
+- formats -- Available seq_io format parsers
+- format_names -- A map between format names and format parsers.
+- format_extensions -- A map between filename extensions and parsers.
+
+"""
+
+# Dev. References :
+#
+#    - http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html
+#    - http://www.ebi.ac.uk/help/formats_frame.html
+#    - http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html
+#    - http://bioperl.org/HOWTOs/html/SeqIO.html
+#    - http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
+#    - http://www.cse.ucsc.edu/research/compbio/a2m-desc.html (a2m)
+#    - http://www.genomatix.de/online_help/help/sequence_formats.html
+
+from corebio.seq import *
+
+import clustal_io
+import fasta_io
+import msf_io
+import nbrf_io
+import nexus_io
+import plain_io
+import phylip_io
+#import null_io
+import stockholm_io
+import intelligenetics_io
+import table_io
+import array_io
+import genbank_io
+
+__all__ = [
+    'clustal_io', 
+    'fasta_io',
+    'msf_io',
+    'nbrf_io',
+    'nexus_io',
+    'plain_io',
+    'phylip_io',
+    'null_io',
+    'stockholm_io',
+    'intelligenetics_io',
+    'table_io',
+    'array_io',
+    'genbank_io',
+    'read',
+    'formats',
+    'format_names',
+    'format_extensions',
+    ]
+
+formats = ( clustal_io, fasta_io, plain_io, msf_io, genbank_io,nbrf_io, nexus_io, phylip_io, stockholm_io, intelligenetics_io, table_io, array_io)
+"""Available seq_io formats"""
+
+
+def format_names() :   
+    """Return a map between format names and format modules"""
+    global formats
+    fnames = {}
+    for f in formats :
+        for name in f.names :
+            assert name not in fnames # Insanity check
+            fnames[name] = f  
+    return fnames
+
+def format_extensions() :   
+    """Return a map between filename extensions and sequence file types"""
+    global formats
+    fext = {}
+    for f in formats :
+        for ext in f.extensions :
+            assert ext not in fext # Insanity check
+            fext[ext] = f  
+    return fext
+
+    
+# seq_io._parsers is an ordered list of sequence parsers that are tried, in 
+# turn, on files of unknown format. Each parser must raise an exception when
+# fed a format further down the list.
+#
+# The general trend is most common to least common file format. However, 
+# 'nbrf_io' is before 'fasta_io' because nbrf looks like fasta with extras, and
+# 'array_io' is last, since it is very general.
+_parsers = (nbrf_io, fasta_io, clustal_io, phylip_io, genbank_io, stockholm_io, msf_io, nexus_io, table_io, array_io)
+
+ 
+def _get_parsers(fin) :
+    global _parsers
+    
+    fnames = format_names()
+    fext = format_extensions()
+    parsers = list(_parsers)
+    best_guess = parsers[0]
+    
+    # If a filename is supplied use the extension to guess the format.
+    if hasattr(fin, "name") and '.' in fin.name :
+        extension = fin.name.split('.')[-1]
+        if extension in  fnames:
+            best_guess = fnames[extension]
+        elif extension in fext :
+            best_guess = fext[extension]
+        
+    if best_guess in parsers :
+        parsers.remove(best_guess)
+    parsers.insert(0,best_guess)
+
+    return parsers
+
+ 
+    
+def read(fin, alphabet=None) :
+    """ Read a sequence file and attempt to guess its format. 
+    First the filename extension (if available) is used to infer the format.
+    If that fails, then we attempt to parse the file using several common   
+    formats.
+    
+    returns :
+        SeqList
+    raises :
+        ValueError - If the file cannot be parsed.
+        ValueError - Sequence do not conform to the alphabet.
+    """
+
+    alphabet = Alphabet(alphabet)
+    parsers =  _get_parsers(fin)
+    
+    for p in _get_parsers(fin) :
+        try:    
+            return p.read(fin, alphabet)
+        except ValueError:
+            pass
+        fin.seek(0)             # FIXME. Non seakable stdin? 
+            
+    names = ", ".join([ p.names[0] for p in parsers])
+    raise ValueError("Cannot parse sequence file: Tried %s " % names)
+
+
+
+
+
+