o Df@svddlmZddlmZmZmZddlmZddlmZddl m Z GdddZ Gd d d e Z Gd d d e Z d S))PathLike)UnionBinaryIOOptional)xopen)Sequence)_is_pathc@sZeZdZedfdeeeefdee fddZ defddZ dd d Z d d Z d dZdS) FileWriterNfile _close_filecCs2t|r||d|_d|_dS||_t||_dS)NwbT)r _file_close_on_exitbool)selfr openerr rV/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/dnaio/writers.py__init__ s   zFileWriter.__init__returncCsd|jjt|jd|jS)Nz{}({!r})name)format __class____name__getattrrrrrr__repr__szFileWriter.__repr__cCs|jr |jdSdSN)rrcloserrrrrszFileWriter.closecCs|jjrtd|S)NzI/O operation on closed file)rclosed ValueErrorrrrr __enter__szFileWriter.__enter__cGs |dSr)r)rargsrrr__exit__$s zFileWriter.__exit__)rN)r __module__ __qualname__rrrstrrrrrrrr"r$rrrrr s    r csjeZdZdZdedfdeeeefde e de e ffdd Z defd d Z dd e efd d ZZS) FastaWriterz4 Write FASTA-formatted sequences to a file. Nr line_lengthr cs.tj|||d|dkr||_dSd|_dS)zm If line_length is not None, the lines will be wrapped after line_length characters. rr rN)superrr))rr r)rr rrrr-s zFastaWriter.__init__rcCdt|jd|jS)NzFastaWriter('{}')rrrrrrrrr;zFastaWriter.__repr__sequencecCs|dur |j}|j}n|}|jdurI|jd|ddg}tdt||jD]}|||||jdq*|jd |ddSd|d|d}|j|ddS)aWrite an entry to the 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(Sequence("name", "ACCAT")) N> asciir) rr0r)rwriteencoderangelenappendjoin)rZname_or_recordr0rsitextrrrr5>s  zFastaWriter.writer)rr%r&__doc__rrrr'rrintrrrr5 __classcell__rrr,rr((s r(cseZdZdZdZdedfdeeee fde de e ffdd Z d efd d Z d ed dfddZd ed dfddZdededed dfddZZS) FastqWriterz Write sequences with qualities in FASTQ format. FASTQ files are formatted like this: @read name SEQUENCE + QUALITIS r FNr two_headersr cs6tj|||d||_|jr|j|_dS|j|_dS)Nr*)r+rZ _two_headers_write_two_headers_writer5)rr rBrr r,rrrhszFastqWriter.__init__rcCr-)NzFastqWriter('{}')rr.rrrrrsr/zFastqWriter.__repr__recordcC|j|dS)z= Write a Sequence record to the FASTQ file. N)rr5Z fastq_bytesrrErrrrDvzFastqWriter._writecCrF)z{ Write a Sequence record to the FASTQ file, repeating the header in the third line after the "+" . N)rr5Zfastq_bytes_two_headersrGrrrrC}rHzFastqWriter._write_two_headersrr0 qualitiescCs |jd|||ddS)Nz@{0:s} {1:s} + {2:s} r3)rr5rr6)rrr0rIrrrwriteseqs zFastqWriter.writeseq)rr%r&r>Z file_moderrrr'rrrrrrrDrCrJr@rrr,rrA\s"   "rAN)osrtypingrrrrr4rZ_utilr r r(rArrrrs    4