B b@sRdZddlmZddlmZmZddlZGdddZGdddeZ d d Z dS) zParse XMS motif files.)motifs)minidomNodeNc@s8eZdZdZddZddZddZdd Zd d Zd S) XMSScannerz Class for scanning XMS XML file.cCs6t|_x(|dD]}|jtjkr||qWdS)zDGenerate motif Record from xms document, an XML-like motif pfm file.motifN)RecordrecordgetElementsByTagNamenodeTyper ELEMENT_NODE handle_motif)selfdocchildr-lib/python3.7/site-packages/Bio/motifs/xms.py__init__s zXMSScanner.__init__cs|||d}ggggdx8|dD]*}fddtdddd g||Dq*Wtjd d }||_|j|d S) zHRead the motif's name and column from the node and add the motif record.name)ACGTcolumncs"g|]\}}|t|qSr)appendfloat).0Z nucleotideZnucleotide_count)nucleotide_countsrr !sz+XMSScanner.handle_motif..rrrrZGATC)ZalphabetZcountsN) get_textr zipget_acgtrZMotifrrr)r nodeZ motif_namerrr)rrr s zXMSScanner.handle_motifcCszxt|dD]f}d}d}xP|jD]F}|jtjkr2q |jdkrP||g|krPd}|jdkr ||g}q W|r |Sq WdS)zCExtract the value of the motif's property named key_name from node.ZpropFNkeyTvalue)r childNodesr rr ZtagNamer)r r!Zkey_nameZ cur_propertyZright_propertyZ cur_valuerrrrget_property_value,s   zXMSScanner.get_property_valuecCsd\}}}}x|dD]}|ddkr|D]6}|jtjkr(||jq |jr |||jq Wt ddd |S)zMReturn a string representation of the motif's properties listed on nodelist .z\s+ ) r rZ TEXT_NODErZ wholeTextZ hasChildNodesrr$resubjoin)r ZnodelistZretlistr!rrrrJs  zXMSScanner.get_textN) __name__ __module__ __qualname____doc__rr r%r rrrrrrs rc@seZdZdZddZdS)rzClass to store the information in a XMS matrix table. The record inherits from a list containing the individual motifs. cCsddd|DS)N css|]}t|VqdS)N)str)rrrrr ]sz!Record.__str__..)r/)r rrr__str__\szRecord.__str__N)r0r1r2r3r7rrrrrVsrcCst|}t|j}|S)zRead motifs in XMS matrix format from a file handle. XMS is an XML format for describing regulatory motifs and PSSMs. This format was defined by Thomas Down, and used in the NestedMICA and MotifExplorer programs. )rparserr)ZhandleZxms_docrrrrread`s  r9) r3ZBiorZxml.domrrr-rlistrr9rrrrs  F