U Zwe@sddlZddlmZddlmZmZmZddlmZddlmZddl m Z Gdd d Z Gd d d e e Z Gd d d e e Z dS)N)PathLike)UnionBinaryIOOptional)xopen)SequenceRecord)SingleEndWriterc@sleZdZUdZeed<eddeee efe e dddZ e dd d Z ddd d Zd dZddZdS) FileWriterzR A mix-in that manages opening and closing and provides a context manager _fileNopener _close_file)filercCsJzt|Wn$tk r2||_t||_YnX||d|_d|_dS)NwbT)osfspath TypeErrorr bool_close_on_exit)selfrr rr,lib/python3.8/site-packages/dnaio/writers.py__init__s zFileWriter.__init__returncCs |jjdt|jd|jdS)Nz('name')) __class____name__getattrr rrrr__repr__#szFileWriter.__repr__cCs|jr|jdSN)rr closer!rrrr$&szFileWriter.closecCs|jjrtd|S)NzI/O operation on closed file)r closed ValueErrorr!rrr __enter__*szFileWriter.__enter__cGs |dSr#)r$)rargsrrr__exit__/szFileWriter.__exit__)r __module__ __qualname____doc__r__annotations__rrrstrrrrr"r$r'r)rrrrr s   r csheZdZdZdeddeeeefe e e e dfddZ eddd Z d e ed d d ZZS) FastaWriteraS Write FASTA-formatted sequences to a file While this class can be instantiated directly, the recommended way is to use `dnaio.open` with appropriate arguments unless you need to set the line_length argument. Arguments: line_length: Wrap sequence lines after this many characters (None disables wrapping) N) line_lengthr r)rr0rcs(tj|||d|dkr|nd|_dS)Nr r)superrr0)rrr0r rrrrr?szFastaWriter.__init__rcCsdt|jd|jdS)Nz FastaWriter('rrr r r!rrrr"JszFastaWriter.__repr__)sequencecCs|dkr|j}|j}n|}|jdk r|jd|ddg}tdt||jD] }|||||jdqT|jd |dn&d|d|d}|j|ddS)aWrite a record to the FASTA file. If only one parameter (name_or_record) is given, it must have attributes .name and .sequence, which are then used. Otherwise, the first parameter must be the name and the second the sequence. The effect is that you can write this: writer.write("name", "ACCAT") or writer.write(SequenceRecord("name", "ACCAT")) N> asciir) rr4r0r writeencoderangelenappendjoin)rZname_or_recordr4rsitextrrrr9Ms  zFastaWriter.write)N)rr*r+r,rrrr.rrintrrr"r9 __classcell__rrr2rr/3s  r/cseZdZdZdZdeddeeee fe e e dfddZ ed d d Z edd d dZedd ddZedd ddZeeeddddZZS) FastqWriteraV Write records in FASTQ format While this class can be instantiated directly, the recommended way is to use `dnaio.open` with appropriate arguments unless you need to set two_headers to True. Arguments: two_headers: If True, the header is repeated on the third line of each record after the "+". rFN) two_headersr r)rrErcs6tj|||d||_t|d|jr*|jn|jdS)Nr r9)r1rZ _two_headerssetattr_write_two_headers_write)rrrEr rr2rrrzszFastqWriter.__init__rcCsdt|jd|jdS)Nz FastqWriter('rrr3r!rrrr"szFastqWriter.__repr__)recordrcCs dstdS)3 Write a record to the FASTQ file. FN)AssertionErrorrrIrrrr9szFastqWriter.writecCs|j|dS)rJNr r9Z fastq_bytesrLrrrrHszFastqWriter._writecCs|j|jdddS)zr Write a record to the FASTQ file, repeating the header in the third line after the "+" . T)rENrMrLrrrrGszFastqWriter._write_two_headers)rr4 qualitiesrc Cs0|jd|dd|dd|ddddS)N@r?r6z + r7)r r9r:)rrr4rNrrrwriteseqszFastqWriter.writeseq)rr*r+r,Z file_moderrrr.rrrrr"rr9rHrGrPrCrrr2rrDks  rD)rrtypingrrrrr8rZ interfacesr r r/rDrrrrs    (8