diff corebio/seq_io/table_io.py @ 4:4d47ab2b7bcc

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/seq_io/table_io.py	Fri Jan 13 07:18:19 2012 -0500
@@ -0,0 +1,126 @@
+#!/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 sequence information in tab delimited format.
+
+This very simple format has two columns per line. The first column is a sequence name, the second column is the sequence itself. The columns are separated by a single tab ("\\t") character.
+
+"""
+from corebio.utils import *
+from corebio.seq import *
+from corebio.seq_io import *
+
+
+names = ( 'table', 'tab')
+extensions = ('tbl')
+
+
+example = """
+EC0001	MKRISTTITTTITITTGNGAG
+EC0002	MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAM
+EC0003	MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLG
+EC0004	MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLD
+EC0005	MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGH
+EC0006	MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLM
+EC0007	MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNS
+EC0008	MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRK
+EC0009	MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDE
+EC0010	MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQ
+"""    
+
+
+
+
+def read(fin, alphabet=None): 
+    """Read and parse 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 a 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)
+
+    for lineno, line in enumerate(fin) :
+        line = line.strip()
+        if line == '' : continue
+
+        columns = line.split('\t')
+        if len(columns) !=2 :
+            raise ValueError( "Parse failed on line %d: did not find two "
+             "columns seperated by a tab."  % (lineno) )        
+        yield Seq(columns[1], alphabet=alphabet, name=columns[0])
+     
+     
+def write(fout, seqs): 
+    """Write a two column, tab delineated file. 
+
+    Args:
+        fout -- A writable stream.
+        seqs  -- A list of Seq's
+    """      
+    for s in seqs : writeseq(fout, s)
+
+    
+def writeseq(fout, seq):
+    """ Write a single sequence in fasta format.
+
+    Args:
+        afile -- A writable stream.
+        seq  -- A Seq instance
+    """
+    
+    name = seq.name or ''
+    print >>fout, name, '\t', seq
+
+    
+    
+    
+    
+     
+
+
+    
+    
+    
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