ó ZIc@s\dZddlmZmZdd d„ƒYZdd d„ƒYZdefd„ƒYZd S( sÅ AlignIO support module (not for general use). Unless you are writing a new parser or writer for Bio.AlignIO, you should not use this module. It provides base classes to try and simplify things. iÿÿÿÿ(tsingle_letter_alphabettGappedtAlignmentIteratorcBs/eZdZded„Zd„Zd„ZRS(s²Base class for building Alignment iterators. You should write a next() method to return Aligment objects. You may wish to redefine the __init__ method as well. cCs||_||_||_dS(sCreate an AlignmentIterator object. handle - input file count - optional, expected number of records per alignment Recommend for fasta file format. alphabet - optional, e.g. Bio.Alphabet.generic_protein Note when subclassing: - there should be a single non-optional argument, the handle, and optional count and alphabet IN THAT ORDER. - you do not have to require an alphabet (?). - you can add additional optional arguments.N(thandletrecords_per_alignmenttalphabet(tselfRt seq_countR((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyt__init__s  cCstdƒ‚dS(s‹Return the next alignment in the file. This method should be replaced by any derived class to do something useful.s This object should be subclassedN(tNotImplementedError(R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pytnext-scCst|jdƒS(s`Iterate over the entries as Alignment objects. Example usage for (concatenated) PHYLIP files: myFile = open("many.phy","r") for alignment in PhylipIterator(myFile) : print "New alignment:" for record in alignment : print record.id print record.seq myFile.close()N(titerR tNone(R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyt__iter__9s N(t__name__t __module__t__doc__R RRR R (((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyRs   tAlignmentWritercBs)eZdZd„Zd„Zd„ZRS(s™Base class for building Alignment writers. You should write a write_alignment() method. You may wish to redefine the __init__ method as wellcCs ||_dS(N(R(RR((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyRMscCstdƒ‚dS(sYUse this to write an entire file containing the given alignments. alignments - A list or iterator returning Alignment objects In general, this method can only be called once per file. This method should be replaced by any derived class to do something useful. It should return the number of alignmentss This object should be subclassedN(R (Rt alignments((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyt write_filePs cCs?|}x&ddgD]}|j|dƒ}qW|jddƒS(s1Use this to avoid getting newlines in the output.s s t s (treplace(Rttexttanswertx((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pytclean_s(RRRRRR(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyRGs  tSequentialAlignmentWritercBs;eZdZd„Zd„Zd„Zd„Zd„ZRS(sÝBase class for building Alignment writers. This assumes each alignment can be simply appended to the file. You should write a write_alignment() method. You may wish to redefine the __init__ method as wellcCs ||_dS(N(R(RR((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyRmscCsF|jƒd}x%|D]}|j|ƒ|d7}qW|jƒ|S(sÉUse this to write an entire file containing the given alignments. alignments - A list or iterator returning Alignment objects In general, this method can only be called once per file.ii(t write_headertwrite_alignmentt write_footer(RRtcountt alignment((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyRps    cCsdS(s‚Use this to write any header. This method should be replaced by any derived class to do something useful.N((R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyR~scCsdS(s‚Use this to write any footer. This method should be replaced by any derived class to do something useful.N((R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyR…scCstdƒ‚dS(sŠUse this to write a single alignment. This method should be replaced by any derived class to do something useful.s This object should be subclassedN(R (RR((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyRŒs(RRRRRRRR(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyRfs     N(((Rt Bio.AlphabetRRRRR(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.pyt s9