z.Ic@sxdZddlZddlmZddlmZddlmZddlmZddZ d efd YZ dS( s Code to deal with alignments written in Fasta format (OBSOLETE). This module is considered obsolete and likely to be deprecated. Please use Bio.AlignIO instead for reading and writing alignments in FASTA format. This mostly just uses the regular Fasta parsing stuff written by Jeff to deal with all of the input and output formats. functions: o parse_file() classes: FastaAlignmentiN(t Alignment(tAlphabet(tIUPAC(tFastatDNAcCs|jdkrtj}nL|jdkr<tj}n.|jdkrZtj}ntd|ttj|}t |d}t j }t j ||}|j }x,|r|j|j|j|j }qW|S(sParse the given file into a FastaAlignment object. Arguments: o file_name - The location of the file to parse. o type - The type of information contained in the file. RtRNAtPROTEINs0Invalid type %s passed. Need DNA, RNA or PROTEINtr(tupperRt ambiguous_dnat ambiguous_rnatproteint ValueErrortFastaAlignmentRtGappedtopenRt RecordParsertIteratortnextt add_sequencettitletsequence(t file_namettypetalphabett fasta_alignt align_filetparsertiteratort cur_align((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Fasta/FastaAlign.pyt parse_files"       R cBs/eZdZejejdZdZRS(sWork with the Fasta Alignment format. The fasta alignment format is basically the same as the regular ol' Fasta format we know and love, except the sequences have gaps (represented by -'s). cCstj||dS(N(Rt__init__(tselfR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Fasta/FastaAlign.pyRAscCspd}xV|jD]K}tj}|j|_|jj|_|t|t j t j }qW|j t j S(s0Print out a fasta version of the alignment info.t( t_recordsRtRecordt descriptionRtseqtdataRtstrtostlineseptrstrip(R t return_stringtitemt new_f_record((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Fasta/FastaAlign.pyt__str__Ds  "( t__name__t __module__t__doc__RRRR RR.(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Fasta/FastaAlign.pyR :s( R1R(tBio.Align.GenericRtBioRt Bio.AlphabetRRRR (((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Fasta/FastaAlign.pyts  "