o Rŀg@szdZddlmZddZGdddeZddZd d Zd d Zd dZ ddZ ddZ e dkr;ddl mZedSdS)z4Module for the support of MEME minimal motif format.)motifsc Csd}t}t||t||t|| |D] }|dr nq|S|d}|d7}t|\}}}t||}tj |j |d} |j | _ || _ || _ || _|| _|| t||ks^Jq)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_numberrecordlinerrrrrmotifrF/var/www/html/myenv/lib/python3.10/site-packages/Bio/motifs/minimal.pyread s0       rc@s eZdZdZddZddZdS)rz4Class for holding the results of a minimal MEME run.cCs(d|_d|_d|_d|_i|_g|_dS)zInitialize record class values.N)versiondatafilecommandrr sequences)selfrrr__init__Ks  zRecord.__init__cCs6t|tr|D] }|j|kr|SqdSt||S)zReturn the motif of index key.N) isinstancestrrlist __getitem__)r$keyrrrrr)Ts   zRecord.__getitem__N)__name__ __module__ __qualname____doc__r%r)rrrrrHs rcCs|D] }|dr nqtdzt|}Wn ty!tdw|}|}t|dt|dt|dt|df\}}}}||||d|_d S) z-Read background letter frequencies (PRIVATE).zBackground letter frequencieszPImproper input file. File should contain a line starting background frequencies.zPUnexpected end of stream: Expected to find line starting background frequencies.r)ACGTN)r ValueErrornext StopIterationstripr floatr)rrrlsr2r3r4r5rrrr as$   4r cCs>|D] }|dr nqtd|}|}|d|_dS)zRead MEME version (PRIVATE).z MEME versionzFImproper input file. File should contain a line starting MEME version.N)r r6r9r r )rrrr;rrrrvs rcCsb|D] }|dr nqtd|dstd||dd}|dkr*d}nd}||_dS) zRead alphabet (PRIVATE).ALPHABETzHUnexpected end of stream: Expected to find line starting with 'ALPHABET'z ALPHABET= z'Line does not start with 'ALPHABET': %srACGTACDEFGHIKLMNPQRSTVWYN)r r6r9replacer)rrralrrrr s    r cCsggggg}|D]J}|}t|dkrn=|dtt|d||dtt|d||dtt|d||dtt|d|qi}|d|d<|d|d<|d|d<|d|d <|S) z)Read letter probability matrix (PRIVATE).rrr<r/r2r3r4r5)r rrroundr:)rrrrfreqscrrrrs       rcCsp|D] }|dr nqt|ddd}t|ddd}t|ddd}|||fS)z Read motif statistics (PRIVATE).zletter-probability matrix:znsites=rrzw=zE=)r intr r:)rrrrrrrrr s  r cCsD|D]}d|vr nqtd|}|}d|dd}|S)zRead motif name (PRIVATE).zsorted by position p-valuez3Unexpected end of stream: Failed to find motif name rr<)r6r9r join)rrwordsrrrr_read_motif_namesrJ__main__) run_doctestN)r.Biorrr(rr rr rr rJr+ Bio._utilsrLrrrrs ;