o Df@sdZddgZddlZddlmZmZmZmZmZddl m Z ddl m Z m Z dd lmZdd lmZGd d d ZGd ddeZGdddeZdS)z+ Classes for reading FASTA and FASTQ files FastaReader FastqReaderN)UnionBinaryIOOptionalIteratorList)xopen) fastq_iterSequence)shorten)FastaFormatErrorc@szeZdZUdZdZdZeed<dZe ed<e dfde e e fde efd d Zd e fd d ZdddZddZddZdS)BinaryFileReaderze A mixin for readers that ensures that a file or a path can be passed in to the constructor. FpairedrbmodeNfile _close_filecCs@t|tr|||j|_d|_dS|rd|_||_dS||_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)selfropenerrrV/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/dnaio/readers.py__init__s    zBinaryFileReader.__init__returncCsd|jjt|jd|jS)Nz{}({!r})name)format __class____name__getattrrrrrr__repr__%szBinaryFileReader.__repr__cCs,|jr|jdur|jd|_dSdSdSN)rrcloser$rrrr'(s  zBinaryFileReader.closecCs|jdur td|S)Nz(I/O operation on closed BinaryFileReader)r ValueErrorr$rrr __enter__-s zBinaryFileReader.__enter__cGs |dSr&)r')rargsrrr__exit__2s zBinaryFileReader.__exit__)rN)r" __module__ __qualname____doc__rrbool__annotations__rrr rrrrr%r'r)r+rrrrrs   $  rcsVeZdZdZdeedfdeeefde de e ffdd Z d e efd d Z ZS) rz! Reader for FASTA files. FNrkeep_linebreaksrcs6tj|||d||_d|_|rd|_dSd|_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 rrF N)superrsequence_classdelivers_qualities _delimiter)rrr1r6rrr!rrr;szFastaReader.__init__rccsd}g}t|j}t|D]I\}}|}|sq|r;|ddkr;|dur2|||j|dV|dd}g}q|rD|ddkrDq|durN||qt d t ||d|duri|||j|dV| dS)zI Read next entry from the file (single entry at a time). Nr>r #z2Expected '>' at beginning of record, but got {!r}.)line) io TextIOWrapperr enumeratestripr6r8joinappendrr _shortendetach)rrseqfir<rrr__iter__Ns0     zFastaReader.__iter__)r"r,r-r.r r rrrr/rrrrH __classcell__rrr9rr6s csVeZdZdZededfdeeefde de e ffdd Z d e efd d ZZS) rzJ Reader for FASTQ files. Does not support multi-line FASTQ files. iNr buffer_sizercstj|||d||_d|_||_t|j|j|j|_zt|j}t |t s)J||_ WdSt y@d|_ t d|_YdStyK|w)zx file is a filename or a file-like object. If file is a filename, then .gz files are supported. r2TFrN)r5rr6r7rJ _fastq_iterr_iternextrr/Z two_headers StopIterationiter Exceptionr')rrr6rJrrthr9rrrss      zFastqReader.__init__rcCs|jSr&)rLr$rrrrHszFastqReader.__iter__)r"r,r-r.r r rrrintrr/rrrHrIrrr9rrns )r.__all__r=typingrrrrrr Z_corer rKr Z_utilr rC exceptionsrrrrrrrrs   '8