:>"^Bã@s°dZddlmZddlmZddlmZddlZdd„ZGdd „d eƒZ d d „Z d d „Z dd„Z dd„Z dd„Zdd„ZdS)z4Module for the support of MEME minimal motif format.é)Úprint_function)ÚSeq)ÚmotifsNc Csd}tƒ}t||ƒt||ƒt||ƒxÚx"|D]}|jdƒr@Pq@W|S|jƒd}|d7}t||ƒ\}}}t||ƒ}tj d|j d|ƒ} |j | _ || _ || _ || _|| _|j| ƒt|ƒ|ks9t‚q9W|S)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 wont retrieve instances, as there are none in minimal meme format. rZMOTIFéÚalphabetÚcounts)ÚRecordÚ _read_versionÚ_read_alphabetÚ_read_backgroundÚ startswithÚsplitÚ_read_motif_statisticsÚ _read_lpmrZMotifrÚ backgroundÚlengthÚnum_occurrencesÚevalueÚnameÚappendÚlenÚAssertionError) ÚhandleZ motif_numberÚrecordÚlinerrrrrÚmotif©rú7/tmp/pip-build-ww9dw3qa/biopython/Bio/motifs/minimal.pyÚreads.            rc@s.eZdZdZdd„Zdd„ZdS)rz4Class for holding the results of a minimal MEME run.cCs:d|_d|_d|_d|_i|_g|_dS)zInitialize record class values.ÚN)ÚversionZdatafileÚcommandrrÚ sequences)ÚselfrrrÚ__init__Ns      zRecord.__init__cCsJt|tƒr6x4|D]}|j|kr|SqWntj||ƒSdS)zReturn the motif of index key.N)Ú isinstanceÚstrrÚlistÚ __getitem__)r#Úkeyrrrrr(Ws   zRecord.__getitem__N)Ú__name__Ú __module__Ú __qualname__Ú__doc__r$r(rrrrrKs  rcCsáx*|D]}|jdƒrPqWtdƒ‚yt|ƒ}Wntk r]tdƒ‚YnX|jƒ}|jƒ}t|dƒt|dƒt|dƒt|dƒf\}}}}d|d |d |d |i|_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.réééÚAÚCÚGÚTN)r Ú ValueErrorÚnextÚ StopIterationÚstripr Úfloatr)rrrÚlsr1r2r3r4rrrr cs     Fr cCsVx*|D]}|jdƒrPqWtdƒ‚|jƒ}|jƒ}|d|_dS)zRead MEME version (PRIVATE).z MEME versionzFImproper input file. File should contain a line starting MEME version.éN)r r5r8r r )rrrr:rrrr ts    r cCsŒx*|D]}|jdƒrPqWtdƒ‚|jdƒsLtd|ƒ‚|jƒjddƒ}|dkryd}nd}||_dS) zRead alphabet (PRIVATE).ZALPHABETzHUnexpected end of stream: Expected to find line starting with 'ALPHABET'z ALPHABET= z'Line does not start with 'ALPHABET': %srZACGTZACDEFGHIKLMNPQRSTVWYN)r r5r8Úreplacer)rrrÚalrrrr €s    r cCsggggg}xÁ|D]¹}|jƒ}t|ƒdkr>P|djtt|dƒdƒƒ|djtt|dƒdƒƒ|djtt|dƒdƒƒ|djtt|dƒdƒƒqWi}|d|d<|d|d<|d|d <|d|d <|S) z)Read letter probability matrix (PRIVATE).éri@Brr;r.r1r2r3r4)r rrÚintr9)rrrZfreqsÚcrrrr‘s  %%%)rcCs—x|D]}|jdƒrPqWt|jdƒdjƒdƒ}t|jdƒdjƒdƒ}t|jdƒdjƒdƒ}|||fS)z Read motif statistics (PRIVATE).zletter-probability matrix:znsites=rrzw=zE=)r r?r r9)rrrrrrrrr¤s ###rcCs_x'|D]}d|krPqWtdƒ‚|jƒ}|jƒ}dj|dd…ƒ}|S)zRead motif name (PRIVATE).zsorted by position p-valuez3Unexpected end of stream: Failed to find motif nameú rr;)r5r8r Újoin)rrÚwordsrrrrÚ_read_motif_name±s     rD)r-Ú __future__rZBiorrÚmathrr'rr r r rrrDrrrrÚs  ;