U  e@sdZddgZddlZddlmZddlmZmZmZm Z m Z ddl m Z dd l m Z mZdd lmZdd lmZdd lmZGd ddZGdddeeZGdddeeZdS)z+ Classes for reading FASTA and FASTQ files FastaReader FastqReaderN)PathLike)UnionBinaryIOOptionalIteratorList)xopen) FastqIterSequenceRecord)shorten)FastaFormatError)SingleEndReaderc@seZdZUdZdZdZeed<dZe ed<e dde e e e feedd d Ze d d d Zdd ddZddZddZdS)BinaryFileReaderze A mixin for readers that ensures that a file or a path can be passed in to the constructor. FpairedrbmodeNopener _close_file)filercCs<t|tr |||j|_d|_n|r2d|_||_n||_dS)z The file is a path or a file-like object. In both cases, the file may be compressed (.gz, .bz2, .xz). TN) isinstancestrr_file_close_on_exit)selfrrrr,lib/python3.8/site-packages/dnaio/readers.py__init__s zBinaryFileReader.__init__returncCs |jjdt|jd|jdS)Nz('namez')) __class____name__getattrrrrrr__repr__/szBinaryFileReader.__repr__cCs$|jr |jdk r |jd|_dSN)rrcloser'rrrr*2s zBinaryFileReader.closecCs|jdkrtd|S)Nz(I/O operation on closed BinaryFileReader)r ValueErrorr'rrr __enter__7s zBinaryFileReader.__enter__cGs |dSr))r*)rargsrrr__exit__<szBinaryFileReader.__exit__)r% __module__ __qualname____doc__rrbool__annotations__rrr rrrrr r(r*r,r.rrrrrs     rcsVeZdZdZdeeddeeee fe e e dfddZ e edd d ZZS) rz Reader for FASTA files While this class can be instantiated directly, the recommended way is to use `dnaio.open` with appropriate arguments. FN)keep_linebreakssequence_classrr)rr4rcsDtj|||d||_d|_|r&dnd|_d|_t|j|_dS)z file is a path or a file-like object. In both cases, the file may be compressed (.gz, .bz2, .xz). keep_linebreaks -- whether to keep newline characters in the sequence rF rN) superr r5delivers_qualities _delimiternumber_of_recordsio TextIOWrapperr)rrr4r5rrr$rrr Hs zFastaReader.__init__r!c cspd}g}|jjrdSt|jD]\}}|}|s4q|r|ddkr|dk r|jd7_z|||j|dVWn6tk r}zt t |d|dW5d}~XYnX|dd}g}q|r|ddkrqq|dk r| |qt dt |d |dq|dk rl|jd7_z|||j|dVWn4tk rj}zt t |ddW5d}~XYnXdS) z> Iterate over the records in this FASTA file. Nr>r z9 (line number refers to record after the problematic one))line#z.Expected '>' at beginning of record, but got 'z'.) rclosed enumeratestripr;r5r:joinr+rrappend_shorten)rr#seqir@errr__iter__^sH   zFastaReader.__iter__)r%r/r0r1r r rrrrr2rr rrK __classcell__rrr>rr@s  csbeZdZdZededdeeee fe e e dfddZ eedd d Zed d ZZS) rz Reader for FASTQ files. Does not support multi-line FASTQ files. While this class can be instantiated directly, the recommended way is to use `dnaio.open` with appropriate arguments. iN)r5 buffer_sizerr)rrMrcstj|||d||_d|_||_zt|j|j|j|_Wntk rZ| YnXz"t |j}t |t svt ||_Wn@tk rd|_td|_Yntk r| YnXdS)zx file is a filename or a file-like object. If file is a filename, then .gz files are supported. rTFrN)r8r r5r9rMr r_iter Exceptionr*nextrr2AssertionErrorZ two_headers StopIterationiter)rrr5rMrrZthr>rrr s.    zFastqReader.__init__r!cCs|jS)z,Iterate over the records in this FASTQ file.)rNr'rrrrKszFastqReader.__iter__cCs&z |jjWStk r YdSXdS)Nr)rNr;AttributeErrorr'rrrr;s zFastqReader.number_of_records)r%r/r0r1r r rrrrintrr2r rrKpropertyr;rLrrr>rrs  &)r1__all__r<osrtypingrrrrr r Z_corer r Z_utilrrG exceptionsrZ interfacesrrrrrrrrs     .J