ó ²“Ic@sldZddlmZdd d„ƒYZdefd„ƒYZdd d„ƒYZd efd „ƒYZd S(sÅ Bio.SeqIO support module (not for general use). Unless you are writing a new parser or writer for Bio.SeqIO, you should not use this module. It provides base classes to try and simplify things. iÿÿÿÿ(tgeneric_alphabettSequenceIteratorcBs,eZdZed„Zd„Zd„ZRS(s³Base class for building SeqRecord iterators. You should write a next() method to return SeqRecord objects. You may wish to redefine the __init__ method as well. cCs||_||_dS(sTCreate a SequenceIterator object. handle - input file alphabet - optional, e.g. Bio.Alphabet.generic_protein Note when subclassing: - there should be a single non-optional argument, the handle. - you do not have to require an alphabet. - you can add additional optional arguments.N(thandletalphabet(tselfRR((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt__init__s cCstdƒ‚dS(sxReturn the next record 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/SeqIO/Interfaces.pytnext(scCst|jdƒS(s(Iterate over the entries as a SeqRecord objects. Example usage for Fasta files: myFile = open("example.fasta","r") myFastaReader = FastaIterator(myFile) for record in myFastaReader : print record.id print record.seq myFile.close()N(titerRtNone(R((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt__iter__3s (t__name__t __module__t__doc__RRRR (((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyRs  tInterlacedSequenceIteratorcBsDeZdZd„Zd„Zd„Zd„Zd„Zd„ZRS(s€Base class for any iterator of a non-sequential file type. This object is not intended for use directly. When writing a parser for any interlaced sequence file where the whole file must be read in order to extract any single record, then you should subclass this object. All you need to do is to define your own: (1) __init__ method to parse the file and call self.move_start() (2) __len__ method to return the number of records (3) __getitem__ to return any requested record. This class will then provide the iterator methods including next(), but relies on knowing the total number of records and tracking the pending record index in as self._n It is up to the subclassed object to decide if it wants to generate a cache of SeqRecords when initialised, or simply use its own lists and dicts and create SeqRecords on request. cCs|jƒtdƒ‚dS(sgCreate the object. This method should be replaced by any derived class to do something useful.s'This object method should be subclassedN(t move_startR(R((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyRWs cCstdƒ‚dS(srReturn the number of records. This method should be replaced by any derived class to do something useful.s'This object method should be subclassedN(R(R((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt__len__bscCstdƒ‚dS(s«Return the requested record. This method should be replaced by any derived class to do something useful. It should NOT touch the value of self._ns'This object method should be subclassedN(R(Rti((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt __getitem__kscCs d|_dS(Ni(t_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/SeqIO/Interfaces.pyRwscCs8|j}|t|ƒkr0|d|_||SdSdS(Ni(RtlenR (Rt next_record((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyRzs   cCst|jdƒS(N(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/SeqIO/Interfaces.pyR ƒs( R R R RRRRRR (((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyR@s  tSequenceWritercBs2eZdZd„Zd„Zd„Zd„ZRS(sÞThis class should be subclassed. Interlaced file formats (e.g. Clustal) should subclass directly. Sequential file formats (e.g. Fasta, GenBank) should subclass the SequentialSequenceWriter class instead. cCs ||_dS(siCreates the writer object. Use the method write_file() to actually record your sequence records.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/SeqIO/Interfaces.pyRŽscCsay|jjƒSWnItk r\|jdkrFtd|jƒ‚q]td|jƒ‚nXdS(s6Use this to catch errors like the sequence being None.s,SeqRecord (id=%s) has None for its sequence.s*SeqRecord (id=%s) has an invalid sequence.N(tseqttostringtAttributeErrorR t TypeErrortid(Rtrecord((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt_get_seq_string”s 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/SeqIO/Interfaces.pytclean¦scCstdƒ‚dS(sìUse this to write an entire file containing the given records. records - A list or iterator returning SeqRecord objects Should return the number of records (as an integer). This method can only be called once.s This object should be subclassedN(R(Rtrecords((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt write_file­s (R R 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/SeqIO/Interfaces.pyR†s    tSequentialSequenceWritercBsDeZdZd„Zd„Zd„Zd„Zd„Zd„ZRS(sùThis class should be subclassed. It is intended for sequential file formats with an (optional) header, repeated records, and an (optional) footer. In this case (as with interlaced file formats), the user may simply call the write_file() method and be done. However, they may also call the write_header(), followed by multiple calls to write_record() and/or write_records() followed finally by write_footer(). Users must call write_header() and write_footer() even when the file format concerned doesn't have a header or footer. This is to try and make life as easy as possible when switching the output format. Note that write_header() cannot require any assumptions about the number of records. cCs(||_t|_t|_t|_dS(N(RtFalset_header_writtent_record_writtent_footer_written(RR((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyRÐs   cCsO|j stdƒ‚|j s,tdƒ‚|j sBtdƒ‚t|_dS(Ns%You have aleady called write_header()s8You have aleady called write_record() or write_records()s%You have aleady called write_footer()(R(tAssertionErrorR)R*tTrue(R((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt write_headerÖscCsM|jstdƒ‚|js*tdƒ‚|j s@tdƒ‚t|_dS(Ns"You must call write_header() firsts9You have not called write_record() or write_records() yets%You have aleady called write_footer()(R(R+R)R*R,(R((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt write_footerÜscCsD|jstdƒ‚|j s+tdƒ‚t|_tdƒ‚dS(sþWrite a single record to the output file. record - a SeqRecord object Once you have called write_header() you can call write_record() and/or write_records() as many times as needed. Then call write_footer() and close().s"You must call write_header() firsts&You have already called write_footer()s This object should be subclassedN(R(R+R*R,R)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/SeqIO/Interfaces.pyt write_recordâs cCsf|jstdƒ‚|j s+tdƒ‚d}x%|D]}|j|ƒ|d7}q8Wt|_|S(sTWrite multiple record to the output file. records - A list or iterator returning SeqRecord objects Once you have called write_header() you can call write_record() and/or write_records() as many times as needed. Then call write_footer() and close(). Returns the number of records written. s"You must call write_header() firsts&You have already called write_footer()ii(R(R+R*R/R,R)(RR$tcountR((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyt write_recordsòs    cCs'|jƒ|j|ƒ}|jƒ|S(sçUse this to write an entire file containing the given records. records - A list or iterator returning SeqRecord objects This method can only be called once. Returns the number of records written. (R-R1R.(RR$R0((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyR%s  ( R R R RR-R.R/R1R%(((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqIO/Interfaces.pyR&»s     N(((R t 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/SeqIO/Interfaces.pyt s 2F5