U _-@sddlZddlZddlZddlmZddlmZddlmZddl Z e dZ e e Ze Zee jee eeedZdZedd d ed D7Zeed 7ZGd ddejZeZdddZdddZdS)N)urllib) constants)AttributeStringErrorz)%(asctime)s - %(levelname)s - %(message)sz\w+=z %;=&,cCsg|] }t|qS)chr).0irr.lib/python3.8/site-packages/gffutils/parser.py 9sr c@seZdZddZdS)QuotercCs(|tkrdt|}n|}|||<|S)Nz%{:02X}) _to_quoteformatord)selfbresrrr __missing__As zQuoter.__missing__N)__name__ __module__ __qualname__rrrrr r@srFcss t|sdSg}tjs(ddkr.|}nFi}|D]8\}}g||<|D]"}||ddd|DqNq:drg} |D]>\} } t| dkr| D]}| | |gfqq| | | fqn t|} fdd } |r| j| d | D]\} } | rR|rt | } d | } | rLd r8d | } d| | g}n| }n&ddkrtd| dg}n| }||qd|}dr|d7}|S)a Reconstructs the original attributes string according to the dialect. Parameters ========== keyvals : dict Attributes from a GFF/GTF feature dialect : dict Dialect containing info on how to reconstruct a string version of the attributes keep_order : bool If True, then perform sorting of attribute keys to ensure they are in the same order as those provided in the original file. Default is False, which saves time especially on large data sets. sort_attribute_values : bool If True, then sort values to ensure they will always be in the same order. Mostly only useful for testing; default is False. rfmtgff3cSsg|] }t|qSr)quoter)rjrrr r qsz _reconstruct.. repeated keyscs0zd|dWStk r*YdSXdS)Norderrg.A)index ValueError)xdialectrr sort_keysz_reconstruct..sort_key)keyzmultival separatorquoted GFF2 valuesz"%s"keyval separatorgtfz""field separatortrailing semicolon;) rrignore_url_escape_charactersitemsappendjoinlenlistsortsorted)Zkeyvalsr$Z keep_orderZsort_attribute_valuespartsZ attributeskvr r.r&valr%Zval_strpartZ parts_strrr#r _reconstructLsR"        r:c sddd}d}|dkr$ttj}d}ddlm}|}|sD||fS|s@|dr\|d }||d }|d |d rg}|D]B}|r|dd kr|d d}|| dd|D} q|ddkrfdd|D} n\|d } g}t |D]F\} }| dkr| r|d d}|| dd|D} q|d} | D]} t | dkrj| \}}n:t | d kr| d}d}n| d}|d  | d d}z ||Wnt k rg||<YnX| r t |dkr |ddkr |ddkr |d d}|rN|d}|||qN|||}||fSg|d<|dd krj|dd}d|d<dD],}||}t |d krn||d <qqnt|drdd|D} d|d<d|d <nbd|d <g}|D]B}|r|dd kr|d d}d|d <|| dqdd|D} | D]} t | dkrN| \}}n:t | d krj| d}d}n| d}|d  | d d}||krd|d <ng||<t |dkr|ddkr|ddkr|d d}d|d<|r |d}t |d kr|d rtd!||||d|q2|d dkrR|drRd"|d<|||}||fS)#a Given the string attributes field of a GFF-like line, split it into an attributes dictionary and a "dialect" dictionary which contains information needed to reconstruct the original string. Lots of logic here to handle all the corner cases. If `dialect` is None, then do all the logic to infer a dialect from this attribute string. Otherwise, use the provided dialect (and return it at the end). cSs>tjs:|ddkr:|D]\}}dd|D}|||<q|S)z Handles the unquoting (decoding) of percent-encoded characters. See notes on encoding/decoding above. rrcSsg|]}tj|qSr)rparseZunquote)rr7rrr r sz:_split_keyvals.._unquote_quals..)rr-r.)qualsr$r&valsZunquotedrrr _unquote_qualss  z&_split_keyvals.._unquote_qualsFNTr)featurer+r,r*r(zleading semicolonrcSs&g|]}|dd|ddfqSr rNr0rprrr r sz"_split_keyvals..rrcsg|]}|qSrsplitrCZkvseprr r scSs&g|]}|dd|ddfqSr@rBrCrrr r sr'r",r)z ; z; r,cSsg|]}|dqS)=rErCrrr r )srLrAcSs&g|]}|dd|ddfqSr@rBrCrrr r 7srzTInternally inconsistent attributes formatting: some have repeated keys, some do not.r))copyrr$gffutilsr?Z dict_classrstriprFr/strip enumerater1r0KeyErrorextend gff3_kw_patmatchr)Z keyval_strr$r>Z infer_dialectr?r<r5piecesrDZkey_valsZleadingsemicolonr Zquoteditemr&r8r=seprrGr _split_keyvalss         *           *    rY)FF)N) rerM collectionsZ six.movesrrNrZgffutils.exceptionsrZloggingZ Formatter formatterZ getLoggerrloggerZ StreamHandlerZchZsetLevelINFOZ setFormatterZ addHandlercompilerTrr0ranger defaultdictrrr:rYrrrr s,         %   e