XffrdZddlZddlmZddlmZddlmZGddZGdd eZ d Z dS) zParse XMS motif files.N)minidom)Node)motifsc0eZdZdZdZdZdZdZdZdS) XMSScannerz Class for scanning XMS XML file.ct|_|dD],}|jtjkr||-dS)zDGenerate motif Record from xms document, an XML-like motif pfm file.motifN)RecordrecordgetElementsByTagNamenodeTyper ELEMENT_NODE handle_motif)selfdocchilds .lib/python3.11/site-packages/Bio/motifs/xms.py__init__zXMSScanner.__init__sYhh --g66 ) )E~!222!!%((( ) )cf||d}ggggd|dD]3}fdtgd||D4t jd}||_|j|dS)zHRead the motif's name and column from the node and add the motif record.name)ACGTcolumncfg|]-\}}|t|.S)appendfloat).0 nucleotidenucleotide_countnucleotide_countss r z+XMSScanner.handle_motif.. sJ   0J 0"*-44U;K5L5LMM   rGATC)alphabetcountsN) get_textr zipget_acgtrMotifrr r)rnode motif_namerr r$s @rrzXMSScanner.handle_motifs]]4#<#T%666=E))dmmUG.D.D.P.P%)N=G++ $ ug 6 6I !     !trc2d\}}}}|dD]}|ddkr$t||g}?|ddkr$t||g}||ddkr$t||g}|ddkr#t||g}||||fS)z1Get and return the motif's weights of A, C, G, T.)r;r;r;weightsymboladeninecytosineguaninethymine)r getAttributer r))rr-acgtr<s rr+zXMSScanner.get_acgt<s' 1a//99 3 3F""8,, 99$--1122$$X..*<<$--1122$$X..);;$--1122$$X..);;$--1122!Qzrc*g}|D]f}|jtjkr||j2|jr-|||jgtj ddd |S)zMReturn a string representation of the motif's properties listed on nodelist .z\s+ ) r r TEXT_NODEr wholeText hasChildNodesr)r3resubjoin)rnodelistretlistr-s rr)zXMSScanner.get_textJs ? ?D}..t~....# ?t}}T_==>>>vfc2777#3#3444rN) __name__ __module__ __qualname____doc__rrr9r+r)rrrrrse**)))"""$    5 5 5 5 5rrceZdZdZdZdS)r zClass to store the information in a XMS matrix table. The record inherits from a list containing the individual motifs. c@dd|DS)zBReturn a string representation of the motifs in the Record object. c34K|]}t|VdS)N)str)r!r s r z!Record.__str__..^s(66U666666r)rO)rs r__str__zRecord.__str__\s#yy66666666rN)rRrSrTrUr\rrrr r Vs- 77777rr cVtj|}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 )handlexms_docr s rreadraas( mF##G  'F Mr) rUrMxml.domrrBiorrlistr rarrrres C5C5C5C5C5C5C5C5L77777T777     r