annotate corebio/seq_io/table_io.py @ 15:981eb8c3a756 default tip

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#!/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 
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#  Software is furnished to do so, subject to the following conditions:
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#  The above copyright notice and this permission notice shall be included
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"""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