Ri :dZddlmZddlmZddlmZddlmZddlm Z ddlm Z ddlm Z dd lm Z dd lm Z dd lmZdd lmZdd lmZddlmZeeefZe e ezezezZeeZeeZGddee e ZdedefdZdedefdZGddee e Zy)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)StringIO)PathLike)AnyStr)Generic)IO)Optional)Union)StreamModeError) MutableSeq)Seq) SeqRecordc peZdZdZeedZ d dedddedzddfdZ ed Z d Z d Z d Z y)SequenceIteratoraBase class for building SeqRecord iterators. You should write a __next__ method that returns the next SeqRecord. You may wish to redefine the __init__ method as well. You must also create a class property `modes` specifying the allowable file stream modes. cy)aNFile modes (binary or text) that the parser can handle. This property must be "t" (for text mode only), "b" (for binary mode only), "tb" (if both text and binary mode are accepted, but text mode is preferred), or "bt" (if both text and binary mode are accepted, but binary mode is preferred). Nselfs L/home/agent/.friday_env/lib/python3.12/site-packages/Bio/SeqIO/Interfaces.pymodeszSequenceIterator.modes, Nsourcealphabetfmtreturncl| td|j}||_t|tr!|d}t |d|z|_||_ y|jd}|dk(r|dk(rt|ddd}n(|d k(r|dk(rt|d dd}n td d||_||_ y) aCreate a SequenceIterator object. Arguments: - source - input file stream, or path to input file - alphabet - no longer used, should be None - fmt - string, mixed case format name for in error messages 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 supportedrrbz% files must be opened in binary mode.trz# files must be opened in text mode.Failed to read from input data) ValueErrorrr isinstance_PathLikeTypesopenstreamreadr RuntimeErrormode)rrrrrr+values r__init__zSequenceIterator.__init__8s(  KL L  fn -8DvsTz2DK$ !KKNE{C<)%DE #C<)%BC "#CD$N DK rcy)z]Return the next SeqRecord. This method must be implemented by the subclass. Nrrs r__next__zSequenceIterator.__next__frc|S)aIterate over the entries as a SeqRecord objects. Example usage for Fasta files:: with open("example.fasta","r") as myFile: myFastaReader = FastaIterator(myFile) for record in myFastaReader: print(record.id) print(record.seq) This method SHOULD NOT be overridden by any subclass. rrs r__iter__zSequenceIterator.__iter__ms  rc|S)Nrrs r __enter__zSequenceIterator.__enter__|s rc |j}|j|jur|jj|`y#t$rYywxYw)NF)r(AttributeErrorrclose)rexc_type exc_value exc_tracebackr(s r__exit__zSequenceIterator.__exit__sN [[F ;;dkk ) KK    K    s A AA)NN)__name__ __module__ __qualname____doc__propertyrr _IOSourcestrr-r/r2r4r;rrrrr#s~   ,,,4Z ,  ,\  rrrecordrct|ts td|jtd|jdt|jt t fstd|jdt|jS)z@Use this to catch errors like the sequence being None (PRIVATE).zExpected a SeqRecord objectzSeqRecord (id=z) has None for its sequence.z) has an invalid sequence.)r%r TypeErrorseqidrr rB)rCs r_get_seq_stringrHsu fi (566 zz. 3OPQQ  S*$5 6. 3MNOO vzz?rtextcF|jddjddS)z;Use this to avoid getting newlines in the output (PRIVATE).   replace)rIs r_cleanrPs <<c " * *4 55rcleZdZdZeedZdeddfdZde de fdZ e d Z d Z d Zd Zy) SequenceWriteraBase class for sequence writers. This class should be subclassed. The user may call the write_file() method to write a complete file containing the sequences. Most subclasses will only need to implement the write_record method. Subclasses must implement the write_records method to include a file header or footer, for file formats that only allow one record, or for file formats that cannot be written sequentially. cy)aNFile modes (binary or text) that the writer can handle. This property must be "t" (for text mode only), "b" (for binary mode only), "tb" (if both text and binary mode are accepted, but text mode is preferred), or "bt" (if both text and binary mode are accepted, but binary mode is preferred). Nrrs rrzSequenceWriter.modesrrtargetrNcjt|tr|jd}t|d|z}ng|}d}d}t ||D]\}} |j |n tdd||jvr |dk(r td|d k(r td ||_ ||_ y#t $rYowxYw) zCreate the writer object.rwtb)r rr#Nr"z#File must be opened in binary mode.r!z!File must be opened in text mode.) r%r&rr'zipwriterEr*r rThandle)rrTr+r(rvaluesr,s rr-zSequenceWriter.__init__s fn -::a=D&#*-FFEF"5&1 O eLL'  O##CD$N4::%3;)*OPPS[)*MNN  !s B&& B21B2rIcF|jddjddS)z1Use this to avoid getting newlines in the output.rKrLrMrN)rrIs rcleanzSequenceWriter.cleans ||D#&..tS99rcnt}||}|g}|j||jS)z(Format the record and return the string.)r write_filegetvalue)clsrCrZwriterrecordss r to_stringzSequenceWriter.to_strings6V('"  rcy)zWWrite a single record to the output file. record - a SeqRecord object Nr)rrCs r write_recordzSequenceWriter.write_recordr0rcDd}|D]}|j||dz }|S)zWrite records to the output file, and return the number of records. records - A list or iterator returning SeqRecord objects r)rf)rrccountrCs r write_recordszSequenceWriter.write_recordss6  F   f % QJE  rc |j|}|j|jur|jj|S#|j|jur|jjwwxYw)zWrite a complete file with the records, and return the number of records. records - A list or iterator returning SeqRecord objects )rjrZrTr7)rrcris rr_zSequenceWriter.write_filese  $&&w/E{{$++- !!# {{$++- !!#.s A5A<)r<r=r>r?r@rrrAr-rBr] classmethodrdrfrjr_rrrrRrRsl   yT8:#:#:!!  rrRN)r?abcrriorosrtypingrrr r r Bior Bio.Seqr r Bio.SeqRecordrrBbytesr&rA _TextIOSource_BytesIOSourcerrHrPrRrrrrws #C' vJ !C '% / # 5!dsGFOdNI#666 \S'&/\r