diff corebio/seq_io/plain_io.py @ 0:c55bdc2fb9fa

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/plain_io.py	Thu Oct 27 12:09:09 2011 -0400
@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+ 
+#  Copyright (c) 2005 Gavin E. Crooks <[e-mail]>
+#
+#  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 raw, unformatted sequence data. The whole file is read 
+in as a sequence.  Whitespace is removed.
+
+
+--- Example Plain/Raw/Text File ---
+
+--------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
+--------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
+--------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
+-----------------------------------YTSDN---------YSGSGDYDSNK
+-SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
+--LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
+-SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
+-EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
+"""
+
+from corebio.seq import *
+from corebio.utils import remove_whitespace
+
+example = """
+--------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
+--------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
+--------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
+-----------------------------------YTSDN---------YSGSGDYDSNK
+-SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
+--LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
+-SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
+-EPC-RDENVHFNRIFLPTIYFIIFLTGIV
+"""
+
+names = ("plain","raw")
+extensions = ('txt',  )
+
+def read(fin, alphabet=None): 
+    """Read a file of raw sequecne data. 
+
+    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) :
+    """ Read the sequence data and yeild one (and only one) sequence.
+
+    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)
+    lines = []    
+    for linenum, line in enumerate(fin) :
+        if line.isspace(): continue # Blank line
+        line = line.strip() 
+        
+        
+        if line[0] == '>' : # probable a fasta file. Fail.
+                raise ValueError(
+                    "Parse Error on input line: %d " % (linenum) )
+        line = remove_whitespace(line)
+        
+        if not alphabet.alphabetic(line) :
+                raise ValueError(
+                    "Character on line: %d not in alphabet: %s : %s" % \
+                     (linenum, alphabet, line) )
+        lines.append(line)
+
+    yield Seq(''.join(lines), alphabet)
+
+
+
+def write(afile, seqs): 
+    """Write raw sequence data, one line per sequence.
+
+    arguments:
+        afile -- A writable stream.
+        seqs  -- A list of Seq's
+    """         
+    for s in seqs :
+        writeseq(afile, s)
+
+    
+def writeseq(afile, seq):
+    """ Write a single sequence in raw format.
+
+    arguments:
+        afile -- A writable stream.
+        seq  -- A Seq instance
+    """
+    print >>afile, seq
+
+            
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