U Zwe;@sdZddgZddlZddlmZddlmZmZmZm Z m Z ddl m Z dd l m Z mZmZdd lmZdd lmZdd lmZGd ddZGdddeeZGdddeeZGdddeeZdS)z+ Classes for reading FASTA and FASTQ files FastaReader FastqReaderN)PathLike)UnionBinaryIOOptionalIteratorList)xopen)BamIter 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, .zst). 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$|jr |jdk r |jd|_dSN)rrcloser(rrr r+2s zBinaryFileReader.closecCs|jdkrtd|S)Nz(I/O operation on closed BinaryFileReader)r ValueErrorr(rrr __enter__7s zBinaryFileReader.__enter__cGs |dSr*)r+)rargsrrr __exit__<szBinaryFileReader.__exit__)r& __module__ __qualname____doc__rrbool__annotations__rrr rrrrr!r)r+r-r/rrrr rs     rcsVeZdZdZdeeddeeee fe e e dfddZ e edd d ZZS) rz Reader for FASTA files While this class can be instantiated directly, the recommended way is to use `dnaio.open` with appropriate arguments. FN)keep_linebreakssequence_classrr)rr5rcsDtj|||d||_d|_|r&dnd|_d|_t|j|_dS)z file is a path or a file-like object. In both cases, the file may be compressed (.gz, .bz2, .xz, .zst). keep_linebreaks -- whether to keep newline characters in the sequence rF rN) superr!r6delivers_qualities _delimiternumber_of_recordsio TextIOWrapperr)rrr5r6rrr%rr r!Hs zFastaReader.__init__r"c cspd}g}|jjrdSt|jD]\}}|}|s4q|r|ddkr|dk r|jd7_z|||j|dVWn6tk r}zt t |d|dW5d}~XYnX|dd}g}q|r|ddkrqq|dk r| |qt dt |d |dq|dk rl|jd7_z|||j|dVWn4tk rj}zt t |ddW5d}~XYnXdS) z> Iterate over the records in this FASTA file. Nr>r z9 (line number refers to record after the problematic one))line#z.Expected '>' at beginning of record, but got 'z'.) rclosed enumeratestripr<r6r;joinr,rrappend_shorten)rr$seqirAerrr __iter__^sH   zFastaReader.__iter__)r&r0r1r2rr rrrrr3rr!rrL __classcell__rrr?r r@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. Nr6 buffer_sizerrrrPrcstj|||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)r9r!r6r:rPr r_iter Exceptionr+nextrr3AssertionError two_headers StopIterationiter)rrr6rPrrZthr?rr r!s.    zFastqReader.__init__r"cCs|jS)z,Iterate over the records in this FASTQ file.rRr(rrr rLszFastqReader.__iter__cCs&z |jjWStk r YdSXdSNrrRr<AttributeErrorr(rrr r<s zFastqReader.number_of_records)r&r0r1r2rr rrrrintrr3r!rrLpropertyr<rMrrr?r rs  &csneZdZdZededdeeee fe e e dfddZ eedd d Zed d Zed dZZS) BamReadera Reader for BAM files. All records in the input BAM must be unmapped single-end reads (with a flag value of 4). While this class can be instantiated directly, the recommended way is to use `dnaio.open` with appropriate arguments. rNNrOrQcsbtj|||d||_d|_||_zt|j|j|_Wntk rV| YnXd|_ dS)NrTF) r9r!r6r:rPr rrRrSr+rV)rrr6rPrrr?rr r!s zBamReader.__init__r"cCs|jS)z*Iterate over the records in this BAM file.rYr(rrr rLszBamReader.__iter__cCs&z |jjWStk r YdSXdSrZr[r(rrr r<s zBamReader.number_of_recordscCs&z |jjWStk r YdSXdS)N)rRheaderr\r(rrr ras zBamReader.header)r&r0r1r2rr rrrrr]rr3r!rrLr^r<rarMrrr?r r_s  r_)r2__all__r=osrtypingrrrrr r Z_corer r rZ_utilrrH exceptionsrZ interfacesrrrrr_rrrr s     .J: