B b@sdZddlmZddlmZddlmZddlmZddlm Z ddl m Z d d Z d d Z d dZddZddZGddde ZdS)zBio.SeqIO support for the "gck" file format. The GCK binary format is generated by the Gene Construction Kit software from Textco BioSoftware, Inc. )unpack)Seq)FeatureLocation) SeqFeature) SeqRecord)SequenceIteratorcCs*||}t||kr&td|d|S)z9Read the specified number of bytes from the given handle.z Cannot read z bytes from handle)readlen ValueError)handlelengthdatar.lib/python3.7/site-packages/Bio/SeqIO/GckIO.py_reads  rcCs*t|d}td|d}t||}||fS)aLRead a length-prefixed packet. Parts of a GCK file are made of "packets" comprising of 4 bytes giving the packet's size, followed by the packet's data. There is no type tag. The type of a packet, and thus the type of data it contains, is solely indicated by the position of the packet within the GCK file. z>Ir)rr)r r rrrr _read_packets  rcCs,t|d}td|d}t||d}|S)zeRead a Pascal string. A Pascal string is one byte for length followed by the actual string. rz>BrASCII)rrdecode)r r rrrr _read_pstring.s rcCs,t|d}td|d}t||d}|S)zcRead a 32-bit Pascal string. Similar to a Pascal string but length is encoded on 4 bytes. rz>Irr)rrr)r r rrrr_read_p4string9s rccsD|d}|stdt|dkr*tdt|\}}td|ddd}||dkr`td|ddd}tt|}t|t|\}}td |dd \}}|t|krtd|d |d krtd xtd|D]}d |d } || | d } td | \} } } }}}}|dkr(d}nd}t | | |d}| dkrJd} nd} i}|dkrnt |}|g|d<|dkrt |}|g|d<|dkrqt || |d}|j |qWt|\}}td |dd \}}|d |dkrtdx^td|D]P}d |d} || | d}td|\} } }}|rIrrz"Conflicting sequence length valuesrz>IH\z9Features packet size inconsistent with number of featuresz>II6xH14xB17xII35xBr)strandZCDSZ misc_featureZlabelZnote)type qualifiersXz3Sites packet size inconsistent with number of sitesz >II24xII48xz>Hii z>16xBZcircularZtopologyZlinear)r r r rrrrrrangerrrrZfeaturesappendrsplitnameidZ descriptionZ annotations)r rZpacketr Z seq_lengthZsequencerecordZ num_featuresioffsetZ feature_datastartendrrZhas_nameZ has_commentversionlocationrr'commentZfeatureZ num_sitesZ site_dataZ num_versionsZversionsZ version_dataflagsZ circularityrrr_parseDs                        r2cs(eZdZdZfddZddZZS) GckIteratorzParser for GCK files.cstj|ddddS)z+Break up a GCK file into SeqRecord objects.bZGCK)modeZfmtN)super__init__)selfsource) __class__rrr7szGckIterator.__init__cCs t|}|S)zStart parsing the file, and return a SeqRecord generator. Note that a GCK file can only contain one sequence, so this iterator will always return a single record. )r2)r8r ZrecordsrrrparseszGckIterator.parse)__name__ __module__ __qualname____doc__r7r; __classcell__rr)r:rr3s r3N)r?ZstructrZBio.SeqrZBio.SeqFeaturerrZ Bio.SeqRecordrZ Interfacesrrrrrr2r3rrrr s