Mercurial > repos > davidmurphy > codonlogo
view corebio/seq_io/table_io.py @ 5:b89bb51eba83
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author | davidmurphy |
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date | Mon, 16 Jan 2012 06:59:52 -0500 |
parents | c55bdc2fb9fa |
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#!/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 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