B ‰°bÜã@sVdZddlmmZddlmZGdd„deƒZdd„Z dd „Z d d „Z d d „Z dS)zAModule for the support of Motif Alignment and Search Tool (MAST).éN)Úmemec@s eZdZdZdd„Zdd„ZdS)ÚRecordaqThe class for holding the results from a MAST run. A mast.Record holds data about matches between motifs and sequences. The motifs held by the Record are objects of the class meme.Motif. The mast.Record class inherits from list, so you can access individual motifs in the record by their index. Alternatively, you can find a motif by its name: >>> from Bio import motifs >>> with open("motifs/mast.crp0.de.oops.txt.xml") as f: ... record = motifs.parse(f, 'MAST') >>> motif = record[0] >>> print(motif.name) 1 >>> motif = record['1'] >>> print(motif.name) 1 cCs(g|_d|_d|_i|_d|_d|_dS)zInitialize the class.ÚN)Ú sequencesÚversionÚdatabaseÚdiagramsÚalphabetÚstrand_handling)Úself©r ú.lib/python3.7/site-packages/Bio/motifs/mast.pyÚ__init__"s zRecord.__init__cCs8t|tƒr(x(|D]}|j|kr|SqWn t ||¡SdS)zReturn the motif of index key.N)Ú isinstanceÚstrÚnameÚlistÚ __getitem__)r ÚkeyÚmotifr r r r+s     zRecord.__getitem__N)Ú__name__Ú __module__Ú __qualname__Ú__doc__rrr r r r r s rcCsLtƒ}yt |¡}Wntjk r2tdƒ‚YnXt||ƒt||ƒ|S)z2Parse a MAST XML format handle as a Record object.zOImproper MAST XML input file. XML root tag should start with ssz"__make_diagram..Z unstrandedcSsg|]\}}d|j›d‘qS)r2r6)r)r7r8r9r r r r:xszStrand handling option z not parsablecSsg|]}|D] }t|ƒ‘q qSr )r)r7ZpairÚsr r r r:€scSsg|]}|dkr|‘qS)Ú0r )r7r;r r r r:„sr4) r*r&r)r%r+rr ÚzipÚ ExceptionÚjoin) rr.Zsequence_lengthZhit_elesZ hit_motifsZgapsZseg_treer8Zhit_posZgapZ motif_strsZ tail_lengthZmotifs_with_gapsr r r r-as0     $ r-) rZxml.etree.ElementTreeZetreeZ ElementTreerZ Bio.motifsrrrr!rrr-r r r r Ús (