B ‰°bÍ6ã@s¢dZddlZddlmZddlmZddlmZddlmZddlm Z ddlm Z dd l m Z Gd d „d eƒZ d d „Zdd„ZGdd„dƒZGdd„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. éN)ÚABC)Úabstractmethod)ÚBiopythonDeprecationWarning)ÚStreamModeError)Ú MutableSeq)ÚSeq)Ú SeqRecordc@s6eZdZdZd dd„Zdd„Zdd „Zed d „ƒZdS) ÚSequenceIteratorzµBase class for building SeqRecord iterators. You should write a parse method that returns a SeqRecord generator. You may wish to redefine the __init__ method as well. NÚtcCsä|dk rtdƒ‚yt|d|ƒ|_d|_Wnztk r¤|dkr`| d¡dkr”td|ƒd‚n4|d kr†| d¡d kr”td |ƒd‚ntd |ƒd‚||_d |_YnXy| |j¡|_Wn&t k rÞ|jrØ|j  ¡‚YnXdS)a³Create a SequenceIterator object. Arguments: - source - input file stream, or path to input file - alphabet - no longer used, should be None This method MAY be overridden by any subclass. Note when subclassing: - there should be a single non-optional argument, the source. - you do not have to require an alphabet. - you can add additional optional arguments. Nz,The alphabet argument is no longer supportedÚrTr rÚz%%s files must be opened in text mode.Úbóz'%s files must be opened in binary mode.zUnknown mode '%s'F) Ú ValueErrorÚopenÚstreamÚshould_close_streamÚ TypeErrorÚreadrÚparseÚrecordsÚ ExceptionÚclose)ÚselfÚsourceZalphabetÚmodeZfmt©rú3lib/python3.7/site-packages/Bio/SeqIO/Interfaces.pyÚ__init__s2   zSequenceIterator.__init__cCs6y t|jƒStk r0|jr*|j ¡‚YnXdS)N)Únextrrrrr)rrrrÚ__next__Hs   zSequenceIterator.__next__cCs|S)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. r)rrrrÚ__iter__PszSequenceIterator.__iter__cCsdS)z8Start parsing the file, and return a SeqRecord iterator.Nr)rÚhandlerrrraszSequenceIterator.parse)Nr N) Ú__name__Ú __module__Ú __qualname__Ú__doc__rr r!rrrrrrr s  )r cCsTt|tƒstdƒ‚|jdkr,td|jƒ‚nt|jttfƒsJtd|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 isinstancerrÚseqÚidrrÚstr)ÚrecordrrrÚ_get_seq_stringfs  r,cCs| dd¡ dd¡S)z;Use this to avoid getting newlines in the output (PRIVATE).Ú ú ú )Úreplace)ÚtextrrrÚ_cleanrsr2c@sNeZdZdZddd„Zdd„Zdd„Zd d „Zd d „Zddd„Z ddd„Z d S)ÚSequenceWriteraiBase 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, as well as for interlaced file formats such as Clustal. The user may call the write_file() method to write a complete file containing the sequences. Alternatively, users may call the write_header(), followed by multiple calls to write_record() and/or write_records(), followed finally by write_footer(). Note that write_header() cannot require any assumptions about the number of records. ÚwcCsÌ|dkrXy| d¡Wn:tk r4tdƒd‚Yq¼tk rPt||ƒ}Yq¼X|}nd|dkr°y| d¡Wn:tk rŒtdƒd‚Yq¼tk r¨t||ƒ}Yq¼X|}n td|ƒ‚||_||_dS) zCreate the writer object.r4r z!File must be opened in text mode.NÚwbrz#File must be opened in binary mode.zUnknown mode '%s')ÚwriterrÚAttributeErrorrÚ RuntimeErrorÚ_targetr")rÚtargetrr"rrrr‰s& zSequenceWriter.__init__cCs| dd¡ dd¡S)z1Use this to avoid getting newlines in the output.r-r.r/)r0)rr1rrrÚclean§szSequenceWriter.cleancCsdS)z)Write the file header to the output file.Nr)rrrrÚ write_header«szSequenceWriter.write_headercCsdS)z)Write the file footer to the output file.Nr)rrrrÚ write_footer³szSequenceWriter.write_footercCs tdƒ‚dS)zWWrite a single record to the output file. record - a SeqRecord object z!This method should be implementedN)ÚNotImplementedError)rr+rrrÚ write_record»szSequenceWriter.write_recordNcCsxd}|dkr.xf|D]}| |¡|d7}qWnFxD|D]<}||kr^|dkrRtdƒ‚n td|ƒ‚| |¡|d7}q4W|S)aWrite records to the output file, and return the number of records. records - A list or iterator returning SeqRecord objects maxcount - The maximum number of records allowed by the file format, or None if there is no maximum. rNézMore than one sequence foundz%Number of sequences is larger than %d)r?r)rrÚmaxcountÚcountr+rrrÚ write_recordsÆs       zSequenceWriter.write_recordsrcCs‚z | ¡| ||¡}| ¡Wd|j|jk r8|j ¡X||kr~|dkrTtdƒ‚n*||krntd||fƒ‚ntd||fƒ‚|S)z”Write a complete file with the records, and return the number of records. records - A list or iterator returning SeqRecord objects Nr@zMust have one sequencez'Number of sequences is %d (expected %d)z0Number of sequences is %d (expected at least %d))r<rCr=r"r9rr)rrZmincountrArBrrrÚ write_fileßs       zSequenceWriter.write_file)r4)N)rN) r#r$r%r&rr;r<r=r?rCrDrrrrr3ws  r3csJeZdZdZd‡fdd„ Zdd„Zdd„Zd d „Zd d „Zd d„Z ‡Z S)ÚSequentialSequenceWritera,Base class for sequential sequence writers (DEPRECATED). This class should be subclassed. It is no longer used. It was intended for sequential file formats with an (optional) header, repeated records, and an (optional) footer. It would enforce callign the methods in appropriate order. To update code using ``SequentialSequenceWriter``, just subclass ``SequenceWriter`` and drop the ``._header_written`` etc checks (or reimplement them). 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. r4cs0tƒ ||¡d|_d|_d|_t dt¡dS)zInitialize the class.FztSequentialSequenceWriter has been deprecated, any class subclassing it will need to subclass SequenceWriter instead.N)ÚsuperrÚ_header_writtenÚ_record_writtenÚ_footer_writtenÚwarningsÚwarnr)rr:r)Ú __class__rrrsz!SequentialSequenceWriter.__init__cCs4|jrtdƒ‚|jrtdƒ‚|jr*tdƒ‚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)rGÚAssertionErrorrHrI)rrrrr<%s z%SequentialSequenceWriter.write_headercCs4|jstdƒ‚|jstdƒ‚|jr*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)rGrMrHrI)rrrrr=5s z%SequentialSequenceWriter.write_footercCs.|jstdƒ‚|jrtdƒ‚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)rGrMrIrHr>)rr+rrrr?Es z%SequentialSequenceWriter.write_recordcCsJ|jstdƒ‚|jrtdƒ‚d}x|D]}| |¡|d7}q&Wd|_|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()rr@T)rGrMrIr?rH)rrrBr+rrrrCSs    z&SequentialSequenceWriter.write_recordscCs<z| ¡| |¡}| ¡Wd|j|jk r6|j ¡X|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. N)r<rCr=r"r9r)rrrBrrrrDis    z#SequentialSequenceWriter.write_file)r4) r#r$r%r&rr<r=r?rCrDÚ __classcell__rr)rLrrEþs rE)r&rJÚabcrrZBiorrZBio.SeqrrZ Bio.SeqRecordrr r,r2r3rErrrrÚ s       N