o Rŀgo&@sdZddlmZddlmZddlmZddlmZddlmZddlm Z ddl m Z dd lm Z dd lm Z dd lmZdd lmZdd lmZddlmZeeefZe e eeeefZeeZGdddeeeZdedefddZdedefddZGdddZdS)zBio.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. )ABC)abstractmethod)PathLike)AnyStr)Generic)IO)Iterator)Optional)Union)StreamModeError) MutableSeq)Seq) SeqRecordc @sheZdZdZ   ddedddedeeddf d d Zd d Zd dZ e de e de efddZdS)SequenceIteratorzBase 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. NtsourcealphabetmodefmtreturncCs|durtdt|trt|d||_d|_n7|dkr-|ddkr,t|ddn|d krA|dd kr@t|d dn td |d d||_d|_z ||j|_ WdSt yj|jri|j w)aCreate 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 supportedrTrrz# files must be opened in text mode.bz% files must be opened in binary mode.Unknown mode ''F) ValueError isinstance_PathLikeTypesopenstreamshould_close_streamreadr parserecords Exceptionclose)selfrrrrr(H/var/www/html/myenv/lib/python3.10/site-packages/Bio/SeqIO/Interfaces.py__init__)s>   zSequenceIterator.__init__cCs.zt|jWSty|jr|jw)zReturn the next entry.)nextr$r%r!r r&r'r(r(r)__next__Xs   zSequenceIterator.__next__cCs|S)aIterate over the entries as a SeqRecord objects. Example usage for Fasta files:: with open("example.fasta","r") as myFile: myFastaReader = FastaIterator(myFile) for record in myFastaReader: print(record.id) print(record.seq) This method SHOULD NOT be overridden by any subclass. It should be left as is, which will call the subclass implementation of __next__ to actually parse the file. r(r,r(r(r)__iter__aszSequenceIterator.__iter__handlecCdS)z8Start parsing the file, and return a SeqRecord iterator.Nr()r'r/r(r(r)r#rzSequenceIterator.parse)NrN)__name__ __module__ __qualname____doc__ _IOSourcestrr r*r-r.rrrrrr#r(r(r(r)r"s(  /  rrecordrcCsZt|ts td|jdurtd|jdt|jttfs(td|jdt|jS)z@Use this to catch errors like the sequence being None (PRIVATE).zExpected a SeqRecord objectNzSeqRecord (id=z) has None for its sequence.z) has an invalid sequence.)rr TypeErrorseqidr r r7)r8r(r(r)_get_seq_stringws   r<textcCs|ddddS)z;Use this to avoid getting newlines in the output (PRIVATE).   replace)r=r(r(r)_cleanrCc@sfeZdZdZddededdfddZd edefd d Zd d ZddZ ddZ dddZ dddZ dS)SequenceWriteraiBase class for sequence writers. This class should be subclassed. It is intended for sequential file formats with an (optional) header, repeated records, and an (optional) footer, as well as for interlaced file formats such as Clustal. The user may call the write_file() method to write a complete file containing the sequences. Alternatively, users may call the write_header(), followed by multiple calls to write_record() and/or write_records(), followed finally by write_footer(). Note that write_header() cannot require any assumptions about the number of records. wtargetrrNcCs|dkr%t|trt||}nCz |}|dWn9ty$tddw|dkrJt|tr4t||}n|}z|dWntyItddwtd|d ||_||_dS) zCreate the writer object.rFrz!File must be opened in text mode.Nwbrz#File must be opened in binary mode.rr) rrrwriter9r RuntimeError_targetr/)r'rGrr/r(r(r)r*s2        zSequenceWriter.__init__r=cCs|ddddS)z1Use this to avoid getting newlines in the output.r>r?r@rA)r'r=r(r(r)cleanrDzSequenceWriter.cleancCr0)z)Write the file header to the output file.Nr(r,r(r(r) write_headerr1zSequenceWriter.write_headercCr0)z)Write the file footer to the output file.Nr(r,r(r(r) write_footerr1zSequenceWriter.write_footercCstd)zWWrite a single record to the output file. record - a SeqRecord object z!This method should be implemented)NotImplementedError)r'r8r(r(r) write_recordszSequenceWriter.write_recordcCspd}|dur|D] }|||d7}q|S|D]}||kr,|dkr&tdtd||||d7}q|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. rNzMore than one sequence foundz%Number of sequences is larger than %d)rPr)r'r$maxcountcountr8r(r(r) write_recordss      zSequenceWriter.write_recordsrcCsz||||}|W|j|jur|jn |j|jur(|jww||krI|dkr5td||krAtd||ftd||f|S)zWrite a complete file with the records, and return the number of records. records - A list or iterator returning SeqRecord objects rQzMust have one sequencez'Number of sequences is %d (expected %d)z0Number of sequences is %d (expected at least %d))rMrTrNr/rKr&r)r'r$mincountrRrSr(r(r) write_files.       zSequenceWriter.write_file)rF)N)rN) r2r3r4r5r6r7r*rLrMrNrPrTrVr(r(r(r)rEs  rEN)r5abcrrosrtypingrrrcollections.abcrr r Bior Bio.Seqr r Bio.SeqRecordrr7bytesrr6 _TextIOSourcerr<rCrEr(r(r(r)s*              U