:>"^7" @sOdZddlmZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z dd lmZmZdd lmZGd d d Zd dZddZddZddZddZdededededeiZddZddddZddd d!Zd"d#ZdS)$zBio.SeqIO support for the SnapGene file format. The SnapGene binary format is the native format used by the SnapGene program from GSL Biotech LLC. )datetime)sub)unpack) parseString)Alphabet) as_handle)Seq) SeqFeatureFeatureLocation) SeqRecordc@sFeZdZdZddZddZddZdd Zd S) _PacketIteratora?Iterate over the packets of a SnapGene file. A SnapGene file is made of packets, each packet being a TLV-like structure comprising: - 1 single byte indicating the packet's type; - 1 big-endian long integer (4 bytes) indicating the length of the packet's data; - the actual data. cCs ||_dS)N)handle)selfr r9/tmp/pip-build-ww9dw3qa/biopython/Bio/SeqIO/SnapGeneIO.py__init__&sz_PacketIterator.__init__cCs|S)Nr)rrrr__iter__)sz_PacketIterator.__iter__cCs|jjd}t|dkr*ttd|d}|jjd}t|dkrmtdtd|d}|jj|}t||krtd|||fS)Nz>BrzUnexpected end of packetz>I)r readlen StopIterationr ValueError)rtypelengthdatarrr__next__,s  z_PacketIterator.__next__cCs |jS)N)r)rrrrnext>sz_PacketIterator.nextN)__name__ __module__ __qualname____doc__rrrrrrrrr s    r cCs~|jrtdtd|d|\}}t|jddtj|_|d@rmd|jdB%dsrASCIIZalphabetZcircularZtopologyZlinearN)seqrrrdecoderZ generic_dna annotations)rrrecordflagssequencerrr_parse_dna_packetBs  ! r)cCst|jd}t|d}|dkr@d|jd8sHHHr"ZSnapGenez%The file is not a valid SnapGene fileN)rr$r)rrr&cookieZseq_typeZ exp_versionZ imp_versionrrr_parse_cookie_packetpsr7cCsRt|jd}x6|jdD]%}i}t|ddd}t|d}|rh|g|ds z*_parse_features_packet..-strandzMissing feature locationQerrorzMissing qualifier nameVtextZpredefr? qualifiersr)rr$getElementsByTagName_get_attribute_valuer?r/r r hasAttributeappend_decode attributesvaluer features)rrr&r2featurequalsrr:rDr;locationZsegmentrngstartendZ qualifierqnameZqvaluesrQrrr_parse_features_packet{sH  "    !rZc Cst|jd}x|jdD]}i}t|d}|rS|g|d.rCZ boundStrandr90rrDrZ primer_bindrINrJr) rr$rKrLr/r?r r rRrN) rrr&r2ZprimerrTr0siterVrWrXrDrSrrr_parse_primers_packets& "   r] cCstdd|S)Nz<[^>]+>)r)rHrrrrOsrONcCs@|j|r#t|j|jS|r8t|n|SdS)N)rMrOrPrQr)noder0r9rFrrrrLs rLcCsl|j|}|rO|djrO|djj|jkrOt|djjS|rdt|n|SdS)Nr)rK childNodesZ firstChildZnodeTypeZ TEXT_NODErOrr)rcr0r9rFchildrenrrrr,s r,c cstd}d}d}t|d}xstt|D]_\}\}}}d}|dkr||dkr|td|tkr=t||||q=W|rtd|jstd |VWdQRXdS) zParse a SnapGene file and return a SeqRecord object. Note that a SnapGene file can only contain one sequence, so this iterator will always return a single record. NrTrbFr`z5The file does not start with a SnapGene cookie packetz Empty file.zNo DNA packet in file)r r enumerater r_packet_handlersr#)r r&nemptyrrrrrrSnapGeneIterators  (     rk)r!rrerstructrZxml.dom.minidomrZBiorZBio.FilerZBio.SeqrZBio.SeqFeaturer r Z Bio.SeqRecordr r r)r5r7rZr]rhrOrLr,rkrrrr s0(   6 $