3 7]@szdZddgZddlZddlmZddlmZmZddlm Z dd l m Z Gd d d Z Gd dde ZGd dde ZdS)z+ Classes for reading FASTA and FASTQ files FastaReader FastqReaderN)xopen) fastq_iterSequence)shorten)FastaFormatErrorc@sBeZdZdZdZdZdZedfddZddZ d d Z d d Z dS) BinaryFileReaderze A mixin for readers that ensures that a file or a path can be passed in to the constructor. FrbNcCs2t|tr|||j}d|_n |r(d|_||_dS)z The file is a path or a file-like object. In both cases, the file may be compressed (.gz, .bz2, .xz). TN) isinstancestrmode_close_on_exit_file)selffileopener _close_filer]/home/psgendb/BIRCHDEV/lib-linux-x86_64/python/lib64/python3.6/site-packages/dnaio/readers.py__init__s   zBinaryFileReader.__init__cCs$|jr |jdk r |jjd|_dS)N)rrclose)rrrrr!s zBinaryFileReader.closecCs|jdkrtd|S)Nz(I/O operation on closed BinaryFileReader)r ValueError)rrrr __enter__&s zBinaryFileReader.__enter__cGs |jdS)N)r)rargsrrr__exit__+szBinaryFileReader.__exit__) __name__ __module__ __qualname____doc__rZpairedrrrrrrrrrrr s r cs2eZdZdZdeedffdd ZddZZS)rz! Reader for FASTA files. FNcs0tj|||d||_d|_|r&dnd|_dS)z file is a path or a file-like object. In both cases, the file may be compressed (.gz, .bz2, .xz). keep_linebreaks -- whether to keep newline characters in the sequence )rrF N)superrsequence_classdelivers_qualities _delimiter)rrZkeep_linebreaksr$rr) __class__rrr4szFastaReader.__init__ccsd}g}tj|j}xt|D]\}}|j}|s4q|rv|ddkrv|dk rd|j||jj|dV|dd}g}q|r|ddkrqq|dk r|j|qt dj t ||dqW|dk r|j||jj|dV|j 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 enumeratestripr$r&joinappendr format_shortendetach)rnameseqfir*rrr__iter__@s,   zFastaReader.__iter__) rrrr rrrr8 __classcell__rr)r'rr/s cs2eZdZdZededffdd ZddZZS)rzJ Reader for FASTQ files. Does not support multi-line FASTQ files. iNc stj|||d||_d|_||_t|j|j|j|_yt|j|_ |j dksTt Wn$t k rzd|_ t f|_YnXdS)zx file is a filename or a file-like object. If file is a filename, then .gz files are supported. )rrTFN)TF) r#rr$r% buffer_size _fastq_iterr_iternextZ two_headersAssertionError StopIterationiter)rrr$r:rr)r'rrres zFastqReader.__init__cCs|jS)N)r<)rrrrr8yszFastqReader.__iter__) rrrr rrrr8r9rr)r'rr`s)r __all__r+rZ_corerr;rZ_utilrr2 exceptionsr r rrrrrrs   "1