o Rŀg*@sdZddlmZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z dd l mZd d lmZd d ZddZddZddZd%ddZddZddZeeeedZddZd&dd Zd&d!d"ZGd#d$d$eZdS)'zBio.SeqIO support for the SnapGene file format. The SnapGene binary format is the native format used by the SnapGene program from GSL Biotech LLC. )datetimesub)unpack) parseString)Seq) SeqFeature)SimpleLocation) SeqRecord)SequenceIteratorccs |d}t|dkrdStd|d}|d}t|dkr%tdtd|d}||}t||kr;td|||fVq) a?Iterate over the packets of a SnapGene file. A SnapGene file is made of packets, each packet being a TLV-like structure comprising: - 1 single byte indicating the packet's type; - 1 big-endian long integer (4 bytes) indicating the length of the packet's data; - the actual data. Tr Nz>BrzUnexpected end of packetz>I)readlenr ValueError)handle packet_typelengthdatarH/var/www/html/myenv/lib/python3.10/site-packages/Bio/SeqIO/SnapGeneIO.py_iterates       rcCsb|jrtdtd|d|\}}t|d|_d|jd<|d@r*d|jd<d Sd |jd<d S) z}Parse a DNA sequence packet. A DNA sequence packet contains a single byte flag followed by the sequence itself. z*The file contains more than one DNA packetz>B%dsr ASCIIDNA molecule_typecirculartopologylinearN)seqrrrdecode annotations)rrrecordflagssequencerrr_parse_dna_packet7s r$cCst|d}t|d}|dkrd|jd<nd|jd<t|d}|r+t|d|jd <t|d }|r5||_t|d }|rP|d d d|_||_ |sR|j|_dSdSdS)zParse a 'Notes' packet. This type of packet contains some metadata about the sequence. They are stored as a XML string with a 'Notes' root node. UTF-8Type SyntheticSYNdata_file_divisionUNC LastModifiedz%Y.%m.%ddateAccessionNumberComments r rN) rr_get_child_valuer rstrptimeidsplitname description)rrr!xmltyper,acccommentrrr_parse_notes_packetIs&       r:cCs,td|\}}}}|ddkrtddS)zParse a SnapGene cookie packet. Every SnapGene file starts with a packet of this type. It acts as a magic cookie identifying the file as a SnapGene file. z>8sHHHrSnapGenez%The file is not a valid SnapGene fileN)rrr)rrr!cookieseq_type exp_version imp_versionrrr_parse_cookie_packetfsr@Fc Cszdd|dD\}}|d}|r|d7}|d7}||kr4t|t||d}td||d}||}|St|||d}|S)Ncss|]}t|VqdSN)int).0xrrr rsz"_parse_location..-r )strandr)r3r r) rangespecrGr! is_primerstartendl1l2locationrrr_parse_locationqsrOcs(t|d}|dD]}i}t|ddd}d}tt|ddd}|d kr)d }d } g} d |d D]:} t| dddkr?q4t| d} d7t| ||} | sS| } n |d kr\| | } n| | } t| d}|rn| |gq4t| d kr|d krtfdd| D} d dd| Dg|d<| st d|dD]I}t|ddd}g}|dD]4}| dr|t |j djq| dr|t |j djq| dr|t|j djq|||<qt|d}|rd |vr|g|d <n ||d vr|g|d<t| ||d!}|j|q d S)"zParse a sequence features packet. This packet stores sequence features (except primer binding sites, which are in a dedicated Primers packet). The data is a XML string starting with a 'Features' root node. r%Featurer7 misc_featuredefaultr directionality1NrSegmentstandardgapranger4cs g|] \}}|d|gqS)r rrCir4n_partsrr s z*_parse_features_packet..;css"|] \}}|d|VqdS):Nrr\rrrrEs z)_parse_features_packet..partszMissing feature locationQzMissing qualifier nameerrorVtextpredefrBlabelr7 qualifiers)rrgetElementsByTagName_get_attribute_valuerBrOappendrreversedjoinr hasAttribute_decode attributesvaluerfeatures)rrr!r6featurequalsr7rGrTrNsubpartssegmentrng next_locationr4 qualifierqnameqvaluesrurr^r_parse_features_packetsr             rcCst|d}|dD]_}i}t|d}|r|g|d<g}|dD]G}t|ddd} tt|d d d } | d kr]+>r)rhrrrrss rsNcCs*||r t|j|jS|rt||SrA)rrrsrtrur)noder4rSrfrrrrn s rncCsJ||}|r|djr|djj|jkrt|djjS|r#t||S)Nr)rm childNodes firstChildnodeType TEXT_NODErsrr)rr4rSrfchildrenrrrr0s r0cs0eZdZdZfddZddZddZZS)SnapGeneIteratorzParser for SnapGene files.cstj|ddddS)aParse a SnapGene file and return a SeqRecord object. Argument source is a file-like object or a path to a file. Note that a SnapGene file can only contain one sequence, so this iterator will always return a single record. br;)modefmtN)super__init__)selfsource __class__rrr&szSnapGeneIterator.__init__cCs||}|S)z9Start parsing the file, and return a SeqRecord generator.)iterate)rrrecordsrrrparse0s zSnapGeneIterator.parseccstd}t|}z t|\}}}Wn tytddw|dkr'tdt||||D]\}}}t|}|durC||||q/|jsKtd|VdS)z.Iterate over the records in the SnapGene file.Nz Empty file. z5The file does not start with a SnapGene cookie packetzNo DNA packet in file) r rnext StopIterationrr@_packet_handlersgetr)rrr!packetsrrrhandlerrrrr5s&      zSnapGeneIterator.iterate)__name__ __module__ __qualname____doc__rrr __classcell__rrrrr#s   r)F)NN)rrrerstructrxml.dom.minidomrBio.SeqrBio.SeqFeaturerr Bio.SeqRecordr Interfacesr rr$r:r@rOrrrrsrnr0rrrrrs4          O*