B ‰°b‡ã@s\dZddlmZdd„ZGdd„deƒZdd„Zd d „Zd d „Zd d„Z dd„Z dd„Z dS)z4Module for the support of MEME minimal motif format.é)Úmotifsc CsÆd}tƒ}t||ƒt||ƒt||ƒx˜x|D]}| d¡r0Pq0W|S| ¡d}|d7}t|ƒ\}}}t||ƒ}tj |j |d} |j | _ || _ || _ || _|| _| | ¡t|ƒ|ks*t‚q*W|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. rZMOTIFé)ÚalphabetÚcounts)ÚRecordÚ _read_versionÚ_read_alphabetÚ_read_backgroundÚ startswithÚsplitÚ_read_motif_statisticsÚ _read_lpmrZMotifrÚ backgroundÚlengthÚnum_occurrencesÚevalueÚnameÚappendÚlenÚAssertionError) ÚhandleZ motif_numberÚrecordÚlinerrrrrÚmotif©rú1lib/python3.7/site-packages/Bio/motifs/minimal.pyÚread s.        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)ÚversionZdatafileZcommandrrÚ sequences)ÚselfrrrÚ__init__Ks zRecord.__init__cCs8t|tƒr(x(|D]}|j|kr|SqWn t ||¡SdS)zReturn the motif of index key.N)Ú isinstanceÚstrrÚlistÚ __getitem__)r Úkeyrrrrr%Ts     zRecord.__getitem__N)Ú__name__Ú __module__Ú __qualname__Ú__doc__r!r%rrrrrHs rcCs¤x |D]}| d¡rPqWtdƒ‚y t|ƒ}Wntk rJtdƒ‚YnX| ¡}| ¡}t|dƒt|dƒt|dƒt|dƒf\}}}}||||dœ|_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.rééé)ÚAÚCÚGÚTN)r Ú ValueErrorÚnextÚ StopIterationÚstripr Úfloatr)rrrÚlsr.r/r0r1rrrr as    4r cCs@x |D]}| d¡rPqWtdƒ‚| ¡}| ¡}|d|_dS)zRead MEME version (PRIVATE).z MEME versionzFImproper input file. File should contain a line starting MEME version.éN)r r2r5r r)rrrr7rrrrvs  rcCsdx |D]}| d¡rPqWtdƒ‚| d¡s8td|ƒ‚| ¡ dd¡}|dkrVd}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 r2r5Úreplacer)rrrZalrrrr„s    rcCsàggggg}xš|D]’}| ¡}t|ƒdkr,P|d tt|dƒ|ƒ¡|d tt|dƒ|ƒ¡|d tt|dƒ|ƒ¡|d tt|dƒ|ƒ¡qWi}|d|d<|d|d<|d|d<|d|d <|S) z)Read letter probability matrix (PRIVATE).érrr8r+r.r/r0r1)r rrÚroundr6)rrrrZfreqsÚcrrrr —s   "    r cCsrx|D]}| d¡rPqWt| d¡d ¡dƒ}t| d¡d ¡dƒ}t| d¡d ¡dƒ}|||fS)z Read motif statistics (PRIVATE).zletter-probability matrix:znsites=rrzw=zE=)r Úintr r6)rrrrrrrrr ªs  r cCsFx|D]}d|krPqWtdƒ‚| ¡}| ¡}d |dd…¡}|S)zRead motif name (PRIVATE).zsorted by position p-valuez3Unexpected end of stream: Failed to find motif nameú rr8)r2r5r Újoin)rrZwordsrrrrÚ_read_motif_name·s r@N) r*ZBiorrr$rr rrr r r@rrrrÚs ;