Xf}dZddlmZddlmZddlmZddlmZddlm Z ddl m Z d Z d Z d Zd Zd ZGdde 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) SeqFeature)SimpleLocation) SeqRecord)SequenceIteratorc|||}t||krtd|d|S)z9Read the specified number of bytes from the given handle.z Cannot read z bytes from handle)readlen ValueErrorhandlelengthdatas /lib/python3.11/site-packages/Bio/SeqIO/GckIO.py_readrsC ;;v  D 4yy6BBBBCCC Kcvt|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. >Ir)rrrs r _read_packetrs@61  F D& ! !! $F  D &>rct|d}td|d}t||d}|S)zeRead a Pascal string. A Pascal string is one byte for length followed by the actual string. rz>BrASCIIrrdecoders r _read_pstringr/I 61  F D& ! !! $F  ' ' 0 0D Krct|d}td|d}t||d}|S)zcRead a 32-bit Pascal string. Similar to a Pascal string but length is encoded on 4 bytes. rrrrrrs r_read_p4stringr :rrc#K|d}|stdt|dkrtdt|\}}t d|ddd}||dz krtd|ddd}t t|}t|t|\}}t d |dd \}}|t|krtd|d z |d zkrtd t|D]}d |d zz} || | d z} t d | \} } } }}}}|dkrd}nd}t| | |}| dkrd} nd} i}|dkrt|}|g|d<|dkrt|}|g|d<|dkrt|| |}|j |t|\}}t d |dd \}}|d z |dzkrtdt|D]N}d |dzz} || | dz}t d|\} } }}|rt||rt|Ot|t|d}t d|d}t||dz}t|D]G}|dz} || | dz}t d|ddd}|dkrt|Ht|dt|}|ddx|_|_||_t|d}t d |d}|dkr d!|jd"<n d#|jd"<|VdS)$Nz Empty file.z1Improper header, cannot read 24 bytes from handlerrrz"Conflicting sequence length valuesrz>IH\z9Features packet size inconsistent with number of featuresz>II6xH14xB17xII35xBr)strandCDS misc_featurelabelnote)type qualifiersXz3Sites packet size inconsistent with number of sitesz >II24xII48xz>Hii z>16xBcirculartopologylinear)r r r rrrrrrangerrr rfeaturesappendrsplitnameid description annotations)rrpacketr seq_lengthsequencerecord num_featuresioffset feature_datastartendr+r&has_name has_commentversionlocationr,r9commentfeature num_sites site_data num_versionsversions version_dataflags circularitys r_parserTEs ;;r??D (''' 4yy2~~LMMM!&))NFFfRaRj))!,JFQJ=>>>abbz  ))H s8}} % %F"&))NFF!'vbqbz!:!:ZS]]""=>>> z\B&&&TUUU < ,(,(QVfv{23 FL !<F F BT68[' Q;;FF F!%V<<< !88DD!D a<< ((D#'&Jw  ??$V,,G")Jv  Q;; XDZHHHw''''"&))NFF$UF2A2J77Z zY^##NOOO 9   # #QV6FRK/0 .4]I.N.N+X{  " & ! ! !  # 6 " " "##L$ --a0LV\C/00H < ##S# 56 T<#455a8 ?? 6 " " "  &#  D"jjooa00FK&)F &"  E%((+KQ)3:&&)1:& LLLLLrc(eZdZdZfdZdZxZS) GckIteratorzParser for GCK files.cPt|dddS)z+Break up a GCK file into SeqRecord objects.bGCK)modefmtN)super__init__)selfsource __class__s rr]zGckIterator.__init__s( cu55555rc$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. )rT)r^rrecordss rparsezGckIterator.parses ..r)__name__ __module__ __qualname____doc__r]rc __classcell__)r`s@rrVrVsM66666rrVN)rgstructrBio.SeqrBio.SeqFeaturerr Bio.SeqRecordr Interfacesr rrrr rTrVrrros %%%%%%))))))######((((((    QQQh"r