RizdZddlmZdZGddeZdZdZdZd Z d Z d Z e d k(rdd l mZeyy)z4Module for the support of MEME minimal motif format.)motifscd}t}t||t||t|| |D]}|j dsn|S|j d}|dz }t |\}}}t||||}tj|j|} |j| _ | jj| _ || _|| _|| _|j#| t%||k(sJ)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. rMOTIF)alphabetcounts)Record _read_version_read_alphabet_read_background startswithsplit_read_motif_statistics _read_lpmrMotifr backgroundrlengthnum_occurrencesevaluenameappendlen) handle motif_numberrecordlinerrrrrmotifs J/home/agent/.friday_env/lib/python3.12/site-packages/Bio/motifs/minimal.pyreadr s>L XF&&!66"VV$  Dw' Mzz|A *@*H'666?C foofE!,,||** /   e6{l***% ceZdZdZdZdZy)r z4Class for holding the results of a minimal MEME run.cXd|_d|_d|_d|_i|_g|_y)zInitialize record class values.N)versiondatafilecommandrr sequences)selfs r__init__zRecord.__init__Ks,    r ct|tr|D]}|j|k(s|cSytj ||S)zReturn the motif of index key.N) isinstancestrrlist __getitem__)r(keyrs rr.zRecord.__getitem__TsA c3  !::$ L !##D#. .r N)__name__ __module__ __qualname____doc__r)r.r rr r Hs>/r r c |D]}|jdsg}|D]c}|j}|rN|jt|j dDcgc]\}}|dzdk(r t |c}}cn|s t dn t dtt|j||_ ycc}}w)z-Read background letter frequencies (PRIVATE).zBackground letter frequencies rzPUnexpected end of stream: Expected to find line starting background frequencies.zPImproper input file. File should contain a line starting background frequencies.N) r rstripextend enumeraterfloat ValueErrordictziprr)rrrbackground_freqsifreqs rr r as  ??: ;!  {{}$++,5TZZ_+E '4 1uz"$K $ f ' * ^  S2BCDF#sCc|D]}|jdsn td|j}|j}|d|_y)zRead MEME version (PRIVATE).z MEME versionzFImproper input file. File should contain a line starting MEME version.r7N)r r<striprr$)rrrlss rr r ~sU  ??> *   T   ::r)rrrrrrfreqscs rrrs"b" F   u:? q uU1X@ABq uU1X@ABq uU1X@ABq uU1X@AB c&)n.   S& )*A Hr c|D]}|jdsnjddk7r.t|jddjdnd}|jddk7r.t|jddjdnd}|jd dk7r.t |jd djdnd }|||fS) z Read motif statistics (PRIVATE).zletter-probability matrix:znsites=rrzw=NzE=g)r findintrr;)rrrrrs rrrs ??7 8  59IIi4HB4NDJJy !! $ * * ,Q /0TV59IIdOr4ISD!!$**,Q/ 0tF6:iio6KU4::d#A&,,.q1 2QTF ?F **r c|D]}d|vsn td|j}|j}dj|dd}|S)zRead motif name (PRIVATE).zsorted by position p-valuez3Unexpected end of stream: Failed to find motif namer6rr7)r<rCrjoin)rrwordsrs r_read_motif_namerYs[P '4 / PNOO ::r^sU;8v/T/2E: , "+4  z&Mr