Mercurial > repos > davidmurphy > codonlogo
diff corebio/seq_io/table_io.py @ 7:8d676bbd1f2d
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author | davidmurphy |
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date | Mon, 16 Jan 2012 07:03:36 -0500 |
parents | c55bdc2fb9fa |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/corebio/seq_io/table_io.py Mon Jan 16 07:03:36 2012 -0500 @@ -0,0 +1,126 @@ +#!/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 + + + + + + + + + + + \ No newline at end of file