ó Y_Sc@@szdZddlmZmZddlTddlTddlTdZdZd Z dd „Z dd „Z d „Z d „ZdS(süRead 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. i(tabsolute_importtprint_functioni(t*ittablettabttbls( EC0001 MKRISTTITTTITITTGNGAG EC0002 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAM EC0003 MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLG EC0004 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLD EC0005 MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGH EC0006 MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLM EC0007 MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNS EC0008 MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRK EC0009 MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDE EC0010 MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQ cC@s,gt||ƒD] }|^q}t|ƒS(sÿRead 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 (titerseqtSeqList(tfintalphabettstseqs((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/table_io.pytread;s "cc@sžt|ƒ}x‹t|ƒD]}\}}|jƒ}|dkrCqn|jdƒ}t|ƒdkrwtd|ƒ‚nt|dd|d|dƒVqWd S( s! 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 ts isEParse failed on line %d: did not find two columns separated by a tab.iR tnameiN(tAlphabett enumeratetstriptsplittlent ValueErrortSeq(RR tlinenotlinetcolumns((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/table_io.pyRJs    cC@s"x|D]}t||ƒqWdS(s|Write a two column, tab-delimited file. Args: fout -- A writable stream. seqs -- A list of Seq's N(twriteseq(tfoutR R ((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/table_io.pytwritebs cC@s,|jp d}t||ddd|ƒdS(s| Write a single sequence in fasta format. Args: afile -- A writable stream. seq -- A Seq instance R tseps tfileN(Rtprint(RtseqR((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/table_io.pyRlsN(stablestab(t__doc__t __future__RRtutilsRR tnamest extensionstexampletNoneR RRR(((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/table_io.pyts