B b%@sdZddlmZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z dd l mZd d lmZd d ZddZddZddZddZddZddZeeeedZddZd$ddZd%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. )datetime)sub)unpack) parseString)Seq)FeatureLocation) SeqFeature) SeqRecord)SequenceIteratorccsx|d}t|dkrdStd|d}|d}t|dkrHtdtd|d}||}t||krttd|||fVqWdS)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. r Nz>BrzUnexpected end of packetz>I)readlenr ValueError)handle packet_typelengthdatar3lib/python3.7/site-packages/Bio/SeqIO/SnapGeneIO.py_iterates       rcCs`|jrtdtd|d|\}}t|d|_d|jd<|d@rRd|jd<n d |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 ASCIIZDNAZ molecule_typeZcircularZtopologyZlinearN)seqrrrdecode annotations)rrrecordflagsZsequencerrr_parse_dna_packet6s  rcCst|d}t|d}|dkr,d|jd<n d|jd<t|d}|rVt|d|jd <t|d }|rj||_t|d }|r|d d d|_||_ |s|j|_dS)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. zUTF-8ZTypeZ SyntheticZSYNZdata_file_divisionZUNCZ LastModifiedz%Y.%m.%ddateZAccessionNumberZComments r rN) rr_get_child_valuerrZstrptimeidsplitnameZ description)rrrxmltyperZacccommentrrr_parse_notes_packetHs"      r'cCs,td|\}}}}|ddkr(tddS)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)rrrZcookieZseq_typeZ exp_versionZ imp_versionrrr_parse_cookie_packetesr)cCsddd|dD\}}|d}||krRt|t||d}td||d}||}nt|||d}|S)NcSsg|] }t|qSr)int).0xrrr qsz#_parse_location..-r )strandr)r"rr)Z rangespecr/rstartendl1l2locationrrr_parse_locationps r5cCst|d}x|dD]}i}t|ddd}d}tt|ddd}|d krVd }d } x>|d D]0} t| d } | st| ||} qf| t| ||} qfW| stdx|dD]} t| ddd} g}xx| dD]j}|dr|t |j dj q|dr|t |j dj q|dr|t|j dj qW||| <qWt|d}|rd|krt|g|d<n||dkr|g|d<t | ||d}|j |qWd 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. zUTF-8ZFeaturer%Z misc_feature)defaultr directionality1NZSegmentrangezMissing feature locationQr#zMissing qualifier name)errorVtextZpredefr*label)r% qualifiers)rrgetElementsByTagName_get_attribute_valuer*r5r hasAttributeappend_decode attributesvaluerfeatures)rrrr$featurequalsr%r/r7r4ZsegmentrngZ qualifierZqnameZqvaluesrHr#rrr_parse_features_packet~sJ          rMc Cst|d}x|dD]}i}t|d}|r:|g|d<xf|dD]X}t|ddd}tt|d d d } | d krxd } nd } tt|| |d|d} |j| qFWqWdS)zParse a Primers packet. A Primers packet is similar to a Features packet but specifically stores primer binding features. The data is a XML string starting with a 'Primers' root node. zUTF-8ZPrimerr#r@Z BindingSiter4zMissing binding site location)r=Z boundStrand0)r6r r:Z primer_bind)r%rAN) rrrBrCr*rr5rIrE) rrrr$ZprimerrKr#ZsiterLr/rJrrr_parse_primers_packets$    rO)r cCs tdd|S)Nz<[^>]+>)r)r?rrrrFsrFNcCs0||rt|j|jS|r(t|n|SdS)N)rDrFrGrHr)noder#r6r=rrrrCs   rCcCsP||}|r:|djr:|djj|jkr:t|djjS|rHt|n|SdS)Nr)rBZ childNodesZ firstChildZnodeTypeZ TEXT_NODErFrr)rTr#r6r=Zchildrenrrrr s   r cs0eZdZdZfddZddZddZZS)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()modeZfmtN)super__init__)selfsource) __class__rrrYszSnapGeneIterator.__init__cCs||}|S)z9Start parsing the file, and return a SeqRecord generator.)iterate)rZrZrecordsrrrparses zSnapGeneIterator.parseccstd}t|}yt|\}}}Wntk r@tddYnX|dkrRtdt|||x0|D](\}}}t|}|dk rd||||qdW|jstd|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)rZrrZpacketsrrrZhandlerrrrr]s   zSnapGeneIterator.iterate)__name__ __module__ __qualname____doc__rYr^r] __classcell__rr)r\rrUs rU)NN)NN)rgrrerZstructrZxml.dom.minidomrZBio.SeqrZBio.SeqFeaturerrZ Bio.SeqRecordr Z Interfacesr rrr'r)r5rMrOrbrFrCr rUrrrr s0          :"