RifddZddlZddlmZddlmZddlmZGddZGdd eZ d Z y) zParse XMS motif files.N)minidom)Node)motifsc.eZdZdZdZdZdZdZdZy) XMSScannerz Class for scanning XMS XML file.ct|_|jdD]1}|jtj k(s!|j |3y)zDGenerate motif Record from xms document, an XML-like motif pfm file.motifN)RecordrecordgetElementsByTagNamenodeTyper ELEMENT_NODE handle_motif)selfdocchilds F/home/agent/.friday_env/lib/python3.12/site-packages/Bio/motifs/xms.py__init__zXMSScanner.__init__sEh --g6 )E~~!2!22!!%( )c |j|jd}ggggd}|jdD]M}tgd|j|Dcgc]"\}}||j t |$c}}Ot jd|}||_|jj |ycc}}w)zHRead the motif's name and column from the node and add the motif record.name)ACGTcolumnGATC)alphabetcountsN) get_textr zipget_acgtappendfloatrMotifrr )rnode motif_namenucleotide_countsr nucleotidenucleotide_countr s rrzXMSScanner.handle_motifs]]4#<#>T%6%66==E)dmmUG.D.P%)N==G+ $ ug 6I  7   !rcd\}}}}|jdD]}|jddk(rt|j|g}3|jddk(rt|j|g}c|jddk(rt|j|g}|jddk(st|j|g}||||fS)z1Get and return the motif's weights of A, C, G, T.)r7r7r7weightsymboladeninecytosineguaninethymine)r getAttributer$r )rr&acgtr8s rr"zXMSScanner.get_acgt<s' 1a//9 3F""8, 9$--12$$X.*<$--12$$X.);$--12$$X.);$--12 3!Qzrc@g}|D]r}|jtjk(r|j|j<|j sI|j|j |jttjdddj|S)zMReturn a string representation of the motif's properties listed on nodelist .z\s+ ) r r TEXT_NODEr# wholeText hasChildNodesr r/resubjoin)rnodelistretlistr&s rr zXMSScanner.get_textJsv ?D}}.t~~.##t}}T__=>  ? vvfc2777#344rN) __name__ __module__ __qualname____doc__rrr5r"r rrrrs*)"$  5rrceZdZdZdZy)r zClass to store the information in a XMS matrix table. The record inherits from a list containing the individual motifs. c2djd|DS)zBReturn a string representation of the motifs in the Record object. c32K|]}t|yw)N)str).0r s r z!Record.__str__..^s6U6s)rK)rs r__str__zRecord.__str__\syy6666rN)rNrOrPrQrZrRrrr r Vs  7rr cZtj|}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 rreadr_as' mmF#G  ' 'F Mr) rQrIxml.domrrBiorrlistr r_rRrrrcs4 C5C5L7T7 r