B b@s|dZddlmZddlmZddlmZddlmZGddde Z dd d Z d dZ GdddeZ GdddejZdS)z5Code for calling and parsing ScanProsite from ExPASy.)urlopen) urlencode)handler) ExpatParserc@seZdZdZddZdS)RecordzRepresents search results returned by ScanProsite. This record is a list containing the search results returned by ScanProsite. The record also contains the data members n_match, n_seq, capped, and warning. cCsd|_d|_d|_d|_dS)zInitialize the class.N)n_matchn_seqZcappedZwarning)selfr 5lib/python3.7/site-packages/Bio/ExPASy/ScanProsite.py__init__szRecord.__init__N)__name__ __module__ __qualname____doc__r r r r r rsrhttps://www.expasy.orgxmlc KsP||d}x$|D]\}}|dk r|||<qWt|}d||f}t|} | S)aExecute a ScanProsite search. Arguments: - mirror: The ScanProsite mirror to be used (default: https://www.expasy.org). - seq: The query sequence, or UniProtKB (Swiss-Prot, TrEMBL) accession - output: Format of the search results (default: xml) Further search parameters can be passed as keywords; see the documentation for programmatic access to ScanProsite at https://www.expasy.org/tools/scanprosite/ScanPrositeREST.html for a description of such parameters. This function returns a handle to the search results returned by ScanProsite. Search results in the XML format can be parsed into a Python object, by using the Bio.ExPASy.ScanProsite.read function. )seqoutputNz %s/cgi-bin/prosite/PSScan.cgi?%s)itemsrr) rZmirrorrkeywordsZ parameterskeyvalueZcommandZurlhandler r r scan s   rcCs*t}t}|||||j}|S)zBParse search results returned by ScanProsite into a Python object.)ContentHandlerParserZsetContentHandlerparserecord)rZcontent_handlerZ saxparserrr r r read?s   r c@s"eZdZdZddZdddZdS) rz7Process the result from a ScanProsite search (PRIVATE).cCst|d|_dS)zInitialize the class.TN)rr firsttime)r r r r r Os zParser.__init__rcCs8|jr$|ddddkr$t|d|_t|||S)zRaise an Error if plain text is received in the data. This is to show the Error messages returned by ScanProsite. Nzutf-8zDefine the beginning of a record and stores the search record.rmatchsetrrmatchN)r*appendcontentrrintrr)r nameZattrsr,r r r startElementvs  zContentHandler.startElementcCsh||jkst|jddgkrd|jd}|tjkrDt|j||<n |tjkrZ|j||<n |j||<dS)z$Define the end of the search record.r+r,N) r*popAssertionErrorrrintegersr/r.strings)r r0r,r r r endElements    zContentHandler.endElementcCs|j|7_dS)zStore the record content.N)r.)r r.r r r charactersszContentHandler.charactersN) r rrrr5r6r r1r7r8r r r r res  rN)rrr)rZurllib.requestrZ urllib.parserZxml.saxrZxml.sax.expatreaderrlistrrr rrr r r r s