ó K,TXc@s|ddlZddlZddlZddlZddlZddlmZmZmZm Z ej j dƒddl Z ddl Z ddlmZdZedƒZd„Zd„Zd „Zd „Zd „Zed „Zd „Zd„Zd„Zd„Zd„Zd„Zd„Zed„Z d„Z!d„Z"d„Z#d„Z$d„Z%d„Z&e'dkrxe&ƒndS(iÿÿÿÿN(tlogtpowtfloortexps@/woldlab/castor/home/georgi/programs/meme_4.11.2/meme/lib/python(tgetLogFETPvalues %4.1fe%+04.0fi cCsn|t}t|ƒ}td||ƒ}|dtd| ƒdkrZd}|d7}n|||f}|S(s• Print x with given format given logx. Handles very large and small numbers with prec digits after the decimal. Returns the string to print.i gà?i(t_log10RR(tlogxtprectformattlog10xtetmtstr((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pyt sprint_logxs   cCs@g}x*t|ƒD]}|j|j|ƒƒqWdj|ƒS(Nt(treversedtappendt getComplementtjoin(twordtalphtrcwordtsym((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytget_rcscCs.g}x!|D]}|j|jƒƒq W|S(s2 Extract strings from FASTA sequence records. (Rt getString(tseqststringsts((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytget_strings_from_seqs%s cCs&| }t|ƒ}|jƒ}g|D]}|j|ƒ^q&}|rrgt||ƒD]}|j|ƒ^qWnd} gt|dƒD] } d^q‰} g} g} xo|D]g}|j|ƒ}|}d}xtdt|ƒ|dƒD]ú}xáddgD]Ó}|dkr|n| }d}xot|ƒD]a}||}|||}||kri|d}Pn||kr1|d7}||kr’Pq’q1q1W||krÉ|}||d}|dkrÉPqÉn|sPqqW|dkríPqíqíW| |cd7<| j|ƒ| j|ƒq®W| | | fS(s¹ Return a list of the number of sequences whose minimum Hamming distance to the given word or its reverse complement is X, for X in [0..w]. Also returns a list with the best distance for each sequence. Also returns a list with the offset (1-relative) of the leftmost match to the word in each sequence. (Matches to reverse complement of the word have negative offsets.) Returns: counts, dists, offsets iiiÿÿÿÿN(tlentgetLentgetComprisingIndexesRtNonetxranget encodeStringR(RRRt given_onlytuse_rctwtalenRt eword_giventeword_rct_tcountstdiststoffsetstseqRtmin_distt best_offsettitstrandtewordtdisttjtesymstesym((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytget_min_hamming_dists-sN  "7# $           cCsˆt||||ƒ\}}}t||||ƒ\} } } tt|ƒt|ƒt|ƒ|| ƒ\} } }}| | ||||fS(sX Find the most enriched Hamming distance for given word. Returns (best_dist, best_log_pvalue, pos_dists, pos_offsets, best_p, best_n) Pos_dists[s] is best distance for sequence s. Pos_offsets[s] is offset to the leftmost best match in sequence s. Offsets are 1-relative; match on reverse complement has negative offset. (R7t'get_best_hamming_enrichment_from_countsR(Rtpos_seqstneg_seqsRR#t print_distst pos_countst pos_distst pos_offsetst neg_countst neg_distst neg_offsetst best_disttbest_log_pvaluetbest_ptbest_n((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytget_best_hamming_enrichmentps cCs<tj|ƒ}tj|ƒ}xMtdt|ƒƒD]6}||c||d7<||c||d7R?R@RARJRKR%R3RPRNROt pvalue_recordt neighborst pos_freqst pos_nsitest neg_freqst neg_nsitestpos_neighbor_countstneg_neighbor_countsR&tcoltlettnew_wordtp_countstn_countstnew_pvalue_record((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytget_enrichment_and_neighbors§s<    $1      #$c Cs‘g}g}xxt|dƒD]f}t|||||||ƒ}tj|ƒ} | j|ƒ|j| jƒƒ|jt|ƒƒqW||fS(sk Get PWMs and numbers of sites for each exact Hamming distance. Returns (freqs[d], nsites[d]). i(RHtget_aln_from_dists_and_offsetstsequencetPWMtsetFromAlignmentRtgetFreqR( R%R+R,RRtfreqstnsitestdtalntpwm((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pyRUàs c Cs¢t|ƒ}g}x‰t|ƒD]{}|jgƒ|j||ƒ}xRt|jƒƒD]>} |j| ƒ} ||jt||||||| ƒƒqXWqW|S(s¶ Return neighbor_counts[col][let][dist] list estimated if old_let were replaced by let. List contains estimated counts of sequences containing the neighboring word. (RR!RRRWt#estimate_new_hamming_counts_col_let( RRR*RoRpR%tneighbor_countsRct old_comprisetsymit new_comprise((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pyRVös   $c CsNtj|ƒ}||kr|Sx(t|dƒD]}d} } ||} t||ƒdkrfq0n|||} tt| tg|j|ƒD]} | | ^qƒƒƒ} tt| tg|j|ƒD]} | | ^q̃ƒƒ} ||c| | 8<|dkr#||dc| 7§s(tkeystsort(R¢R¤((R¢sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytsorted_re_pvalue_keys£s  c Cs¼t||||||ƒ\}}|d|ks8| rF|ddfStg|D]}||d|f^qPƒ\} } dG|Gt|ddtƒGdG| Gt| dtƒGH|d| fS(NiRtoriginalisbest neighbor (estimated)(RitminR RI( RRZR9R:RR#R[R\ttmpt best_pvaluet best_word((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytget_best_neighborªs !35c Cs`d}|}xGt||||||ƒ\}}||kr@Pq|}|}|}qW||fS(Ni(R¬( RR9R:RR#RCR«RPtneighbor((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytrefine_consensus¹s!  cCs/d}d}d}t}t}dtjd}ttjƒdkratj|IJtjdƒnd}xè|ttjƒkrQtj|}|dkrÚ|d7}ytj|}WqDtj|IJtjdƒqDXnj|dkr(|d7}ytj|}WqDtj|IJtjdƒqDXn|dkrv|d7}ytj|}WqDtj|IJtjdƒqDXnÎ|dkrÄ|d7}ytj|}WqDtj|IJtjdƒqDXn€|dkry t}WqDtj|IJtjdƒqDXnC|d kr*tj|IJtjdƒntj|IJtjdƒ|d7}qjW|dksj|dkr‡tj|IJtjdƒntjƒ} d} |dkr·t j |ƒ} n t j ƒ} tjd IJt t j|| ƒƒ} t t j|| ƒƒ} |r't|| | | |ƒ\} }n|} tjd IJt| | | | |ƒ\}}}}}}}t|dtƒ}t|ƒ}tjd I|I|I|I|I|Id IJtjd||||fIJt| ƒt| |||| ƒtjƒ}|| }tjd|IJtjd|IJdS(Ns“USAGE: %s [options] -w word (required) -p positive sequences FASTA file name (required) -n negative sequences FASTA file name (required) -a alphabet definition file -r refine consensus by branching search (distance 1 steps; beam size = 1). -h print this usage message Compute the Hamming distance from to each FASTA sequence in the positive and negative files. Apply Fisher's Exact test to each distance. may contain ambiguous characters. iis-ws-ps-ns-as-rs-hsReading sequences...sComputing Hamming alignment...t[t]sEBest ZOOPs alignment has %d sites / %d at distance %d with p-value %sselapsed time: %.2f secondss#elapsed time: %.2f seconds(R tFalseRStargvRRTtexittTruettimeR‘t loadFromFiletdnaRRkt readFASTAR®RŒR RIRšRžR(tpos_seq_file_nametneg_seq_file_nametalphabet_file_nametrefineR#tusageR0targRt start_timeRR9R:R«RCR3RPRNRJRORKRrRQRptend_timetelapsed((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pytmainÈsœ                         ! - 1   t__main__((R”RStstringRGRµtmathRRRRtpathRR‘RkthypergeometricRRIRR RRR7RFR±R8RiRURVRtRjRŠR‹RŒRšRžR¦R¬R®RÂt__name__(((sP/woldlab/castor/home/georgi/programs/meme_4.11.2/scripts/fasta-hamming-enrich.pyts:<"      C  " 9   '         i