o Df8@s dZgdZddlZddlmZmZddlmZddlZddlm Z m Z m Z m Z m Z ddlmZdd lmZmZdd lmZmZdd lmZmZdd lmZmZmZmZdd lmZmZddl m!Z"ddl#m$Z$dddddedde e%ee fde e e%ee fde e%de&de%de e&de eeeeddddddf fd d!Z'd"e%de e%fd#d$Z(dddd%d&e e%ee fde e%de%de e&de eeeeff d'd(Z)d)e de e%fd*d+Z*Gd,ddZ+Gd-ddZ,Gd.ddZ-Gd/dde-Z.Gd0ddZ/Gd1dde/Z0dS)2z@ Sequence I/O: Read and write FASTA and FASTQ files efficiently )openSequence FastaReader FastaWriter FastqReader FastqWriterUnknownFileFormatFileFormatErrorFastaFormatErrorFastqFormatErrorInterleavedSequenceReaderInterleavedSequenceWriterPairedSequenceReader read_chunksread_paired_chunksrecord_names_match __version__N)fspathPathLike) ExitStack)OptionalUnionBinaryIOTupleIterator)xopen)rr)rr)rr)rrr r )rr)version)_is_pathFr)file2 fileformat interleavedmode qualitiesopenerfile1r r!r"r#r$returnr PairedSequenceWriterPairedSequenceAppenderr r InterleavedSequenceAppendercCs|dvrtd|r|durtd|durD|dvr"||kr"td|dkr.t||||dS|d kr;t|||||dSt|||||dS|re|dkrQt|||dS|d kr]t||||dSt||||dSt|||||d S) a Open sequence files in FASTA or FASTQ format for reading or writing. This is a factory that returns an instance of one of the ...Reader or ...Writer classes also defined in this module. file1, file2 -- Paths to regular or compressed files or file-like objects (as str or as pathlib.Path). Use only file1 if data is single-end. If sequences are paired, use also file2. mode -- Either 'r' for reading, 'w' for writing or 'a' for appending. interleaved -- If True, then file1 contains interleaved paired-end data. file2 must be None in this case. fileformat -- If set to None, the file format is autodetected from the file name extension. Set to 'fasta' or 'fastq' to not auto-detect. qualities -- When mode is 'w' and fileformat is None, this can be set to True or False to specify whether the written sequences will have quality values. This is is used in two ways: * If the output format cannot be determined (unrecognized extension etc), no exception is raised, but fasta or fastq format is chosen appropriately. * When False (no qualities available), an exception is raised when the auto-detected output format is FASTQ. opener -- A function that is used to open file1 and file2 if they are not already open file-like objects. By default, xopen is used, which can also open compressed file formats. rwaMode must be 'r', 'w' or 'a'Nz+When interleaved is set, file2 must be Nonewaz)The paired-end output files are identicalr)r%r,r%r!r#r$) ValueErrorr r(r)r r r* _open_single)r&r r!r"r#r$r%r3W/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/dnaio/__init__.pyr*s*3  rnamecCsp|}dD]}||r|dt| }nqtj|\}}|dvr'dS|dvs4|dkr6|dr6dSdS) ze name -- file name Return 'fasta', 'fastq' or None if the format could not be detected. )z.gzz.xzz.bz2N)z.fastaz.faz.fnaz.csfastaz.csfafasta)z.fastqz.fqz.txt _sequencefastq)lowerendswithlenospathsplitext)r5extr3r3r4_detect_format_from_nameys r@)r!r#r$ file_or_pathcCs|dvrtdt|rt|}|||d}d}n"|dkr't|ds'td|}t|dr8t|jtr8|j}nd }d }|dkrBtnt}|dkrJt nt } t j ||d t j | |d d } |r{z | | } W| |Styz|td |w|d urt|}|d ur|dkr|d ur|rdnd}|dkr|d urt|}|d urt|dt|} |td| |d ur|dksJ|d urdnd} |td| |dkr|dvr|d ur|td| ||S)zG Open a single sequence file. See description of open() above. r+r.bTrreadintozQWhen passing in an open file-like object, it must have been opened in binary moder5NF)Z _close_file)r8r6z:File format {!r} is unknown (expected 'fasta' or 'fastq').r,r8r6zCould not determine whether file "{}" is FASTA or FASTQ. The file extension was not available or not recognized and the first character in the file is unexpected.z. because the output file name is not availablez=Auto-detection of the output file format (FASTA/FASTQ) failedr/zDOutput format cannot be FASTQ since no quality values are available.)r1rrhasattr isinstancer5strrrrr functoolspartialr9KeyErrorcloserformatr@_detect_format_from_contentgetattrrepr)rAr%r!r#r$r=fileZ close_fileZ fastq_handlerZ fasta_handlerhandlershandlerr5extrar3r3r4r2sp       r2rPcCsX|r|d}|dkr|ddn |ddd}ddddd}||dS)z) Return 'fasta', 'fastq' or None rrr8r6)@>#N)seekablereadtellseekpeekget)rP first_charformatsr3r3r4rMs    rMc@seZdZdZdZdefdeeee fdeeee fde efddZ d efd d Z d e eeeffd d ZdddZddZddZdS)r z Read paired-end reads from two files. Wraps two BinaryFileReader instances, making sure that reads are properly paired. TNr&r r!cCslt$}|t|||d|_|t|||d|_|j|_Wdn1s*wY|jj|_dSN)r%r!) r enter_contextr2reader1reader2pop_allrK_closedelivers_qualities)selfr&r r!r%stackr3r3r4__init__s zPairedSequenceReader.__init__r'cCsd|j|jS)Nz(PairedSequenceReader(file1={}, file2={}))rLrcrdrhr3r3r4__repr__szPairedSequenceReader.__repr__c cst|jt|j}} zt|}Wnty1z t|tddddty0YYdSwwzt|}WntyFtddddwt|j|js[td|j|jddd||fVq )zY Iterate over the paired reads. Each item is a pair of Sequence objects. TzKReads are improperly paired. There are more reads in file 2 than in file 1.NlinezKReads are improperly paired. There are more reads in file 1 than in file 2.zTReads are improperly paired. 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