XfdZddlmZdZGddeZdZdZdZd Z d Z d Z e d krdd l mZedSdS)z4Module for the support of MEME minimal motif format.)motifsc d}t}t||t||t|| |D]}|drn|S|d}|dz }t |\}}}t||}tj |j |} |j | _ || _ || _ || _|| _|| t#||ksJ)aParse the text output of the MEME program into a meme.Record object. Examples -------- >>> from Bio.motifs import minimal >>> with open("motifs/meme.out") as f: ... record = minimal.read(f) ... >>> for motif in record: ... print(motif.name, motif.evalue) ... 1 1.1e-22 You can access individual motifs in the record by their index or find a motif by its name: >>> from Bio import motifs >>> with open("motifs/minimal_test.meme") as f: ... record = motifs.parse(f, 'minimal') ... >>> motif = record[0] >>> print(motif.name) KRP >>> motif = record['IFXA'] >>> print(motif.name) IFXA This function won't retrieve instances, as there are none in minimal meme format. rTMOTIF)alphabetcounts)Record _read_version_read_alphabet_read_background startswithsplit_read_motif_statistics _read_lpmrMotifr backgroundlengthnum_occurrencesevaluenameappendlen) handle motif_numberrecordlinerrrrrmotifs 2lib/python3.11/site-packages/Bio/motifs/minimal.pyreadr s%>L XXF&&!!!66"""VV$$$+  Dw''  Mzz||A *@*H*H'6?33 fofEEE!, /   e6{{l****%+ceZdZdZdZdZdS)r z4Class for holding the results of a minimal MEME run.cZd|_d|_d|_d|_i|_g|_dS)zInitialize record class values.N)versiondatafilecommandrr sequences)selfs r__init__zRecord.__init__Ks0    r ct|tr|D]}|j|kr|cSdSt||S)zReturn the motif of index key.N) isinstancestrrlist __getitem__)r(keyrs rr.zRecord.__getitem__Ts` c3   / ! !:$$ LLL% ! !##D#.. .r N)__name__ __module__ __qualname____doc__r)r.r rr r Hs8>>/////r r c|D]}|drntd t|}n#t$rtdwxYw|}|}t |dt |dt |dt |df\}}}}||||d|_d S) z-Read background letter frequencies (PRIVATE).zBackground letter frequencieszPImproper input file. File should contain a line starting background frequencies.zPUnexpected end of stream: Expected to find line starting background frequencies.r)ACGTN)r ValueErrornext StopIterationstriprfloatr)rrrlsr9r:r;r<s rr r as   ??: ; ;  E  ^    F||     ^     ::< * *  E  T    ::<>O D!!!$**,,Q/ 0 0F 4::d##A&,,..q1 2 2F ?F **r c|D]}d|vrn td|}|}d|dd}|S)zRead motif name (PRIVATE).zsorted by position p-valuez3Unexpected end of stream: Failed to find motif name rrD)r=r@rjoin)rrwordsrs r_read_motif_namerVsqPP '4 / / E 0NOOO ::<r[s;:888v/////T///2999*   &   & + + +    z&&&&&&KMMMMMr