:>"^b%ã@s¶dZddlmZddlZddlmZddlmZmZddl m Z Gdd„de ƒZ d d „Z d d „ZGd d„de ƒZGdd„deƒZdS)zÄBio.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. é)Úprint_functionN)Úgeneric_alphabet)ÚSeqÚ MutableSeq)Ú SeqRecordc@s\eZdZdZedd„Zdd„ZejddkrLdd „Z d d „Z d S) ÚSequenceIteratorz²Base 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)aöCreate a SequenceIterator object. Arguments: - handle - input file - alphabet - optional, e.g. Bio.Alphabet.generic_protein This method MAY be overridden by any subclass, for example if you need to process a header or accept additional arguments. 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)ÚhandleÚalphabet)Úselfrr ©r ú9/tmp/pip-build-ww9dw3qa/biopython/Bio/SeqIO/Interfaces.pyÚ__init__s zSequenceIterator.__init__cCstdƒ‚dS)zÖReturn the next record in the file. This method's stub-implementation MUST be overridden by any subclass to actually parse the file and return the next entry as a SeqRecord object. z2The subclass should implement the __next__ method.N)ÚNotImplementedError)r r r r Ú__next__/szSequenceIterator.__next__récCs |jƒS)z8Python 2 style alias for Python 3 style __next__ method.)r)r r r r Únext:szSequenceIterator.nextcCst|jdƒS)aIterate over the entries as a SeqRecord objects. Example usage for Fasta files:: with open("example.fasta","r") as myFile: myFastaReader = FastaIterator(myFile) for record in myFastaReader: print(record.id) print(record.seq) This method SHOULD NOT be overridden by any subclass. It should be left as is, which will call the subclass implementation of __next__ to actually parse the file. N)Úiterr)r r r r Ú__iter__>szSequenceIterator.__iter__N) Ú__name__Ú __module__Ú __qualname__Ú__doc__rr rÚsysÚ version_inforrr r r r rs   rcCsxt|tƒstdƒ‚|jdkr@td|jƒ‚n+t|jttfƒsktd|jƒ‚t|jƒS)z@Use this to catch errors like the sequence being None (PRIVATE).zExpected a SeqRecord objectNz,SeqRecord (id=%s) has None for its sequence.z*SeqRecord (id=%s) has an invalid sequence.)Ú isinstancerÚ TypeErrorÚseqÚidrrÚstr)Úrecordr r r Ú_get_seq_stringQs r cCs|jddƒjddƒS)z;Use this to avoid getting newlines in the output (PRIVATE).Ú ú ú )Úreplace)Útextr r r Ú_clean]sr&c@sFeZdZdZdd„Zdd„Zdd„Zdd „Zd S) ÚSequenceWriterzèBase class for building SeqRecord writers. Interlaced file formats (e.g. Clustal) should subclass directly. Sequential file formats (e.g. Fasta, GenBank) should subclass the SequentialSequenceWriter class instead. cCs ||_dS)zqCreate the writer object. Use the method write_file() to actually record your sequence records. N)r)r rr r r r kszSequenceWriter.__init__cCsxt|tƒstdƒ‚|jdkr@td|jƒ‚n+t|jttfƒsktd|jƒ‚t|jƒS)z@Use this to catch errors like the sequence being None (PRIVATE).zExpected a SeqRecord objectNz,SeqRecord (id=%s) has None for its sequence.z*SeqRecord (id=%s) has an invalid sequence.)rrrrrrrr)r rr r r r rs zSequenceWriter._get_seq_stringcCs|jddƒjddƒS)z1Use this to avoid getting newlines in the output.r!r"r#)r$)r r%r r r Úclean|szSequenceWriter.cleancCstdƒ‚dS)zõUse 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. z This object should be subclassedN)r)r Úrecordsr r r Ú write_file€s zSequenceWriter.write_fileN)rrrrr r r(r*r r r r r'bs   r'c@s^eZdZdZdd„Zdd„Zdd„Zdd „Zd d „Zd d „Z dS)ÚSequentialSequenceWriteraBase class for sequence writers. This 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(||_d|_d|_d|_dS)zInitialize the class.FN)rÚ_header_writtenÚ_record_writtenÚ_footer_written)r rr r r r §s   z!SequentialSequenceWriter.__init__cCsO|j stdƒ‚|j s,tdƒ‚|j sBtdƒ‚d|_dS)a4Write the file header. If your file format defines a header, you should implement this method in order to write the header before any of the records. The default implementation checks the private attribute ._header_written to ensure the header is only written once. z%You have aleady called write_header()z8You have aleady called write_record() or write_records()z%You have aleady called write_footer()TN)r,ÚAssertionErrorr-r.)r r r r Ú write_header®s   z%SequentialSequenceWriter.write_headercCsM|jstdƒ‚|js*tdƒ‚|j s@tdƒ‚d|_dS)a0Write the file footer. If your file format defines a footer, you should implement this method in order to write the footer after all the records. The default implementation checks the private attribute ._footer_written to ensure the footer is only written once. z"You must call write_header() firstz9You have not called write_record() or write_records() yetz%You have aleady called write_footer()TN)r,r/r-r.)r r r r Ú write_footer¾s   z%SequentialSequenceWriter.write_footercCsD|jstdƒ‚|j s+tdƒ‚d|_tdƒ‚dS)aWrite 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(). z"You must call write_header() firstz&You have already called write_footer()Tz This object should be subclassedN)r,r/r.r-r)r rr r r Ú write_recordÎs  z%SequentialSequenceWriter.write_recordcCsf|jstdƒ‚|j s+tdƒ‚d}x%|D]}|j|ƒ|d7}q8Wd|_|S)aTWrite 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. z"You must call write_header() firstz&You have already called write_footer()réT)r,r/r.r2r-)r r)Úcountrr r r Ú write_recordsßs    z&SequentialSequenceWriter.write_recordscCs'|jƒ|j|ƒ}|jƒ|S)zçUse 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. )r0r5r1)r r)r4r r r r*õs  z#SequentialSequenceWriter.write_fileN) rrrrr r0r1r2r5r*r r r r r+‘s      r+)rÚ __future__rrZ Bio.AlphabetrZBio.SeqrrZ Bio.SeqRecordrÚobjectrr r&r'r+r r r r Ú s ; /