annotate test-data/meme_output_test1.txt @ 2:3e5c80594237 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"

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MEME - Motif discovery tool
MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)
REFERENCE
TRAINING SET
CONTROL SEQUENCES= --none--
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
chr21_19617074_19617124_ 1.0000     50  chr21_26934381_26934431_ 1.0000     50  
COMMAND LINE SUMMARY
model:  mod=         zoops    nmotifs=         1    evt=           inf
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
width:  minw=            8    maxw=           50
nsites: minsites=        2    maxsites=       30    wnsites=       0.8
theta:  spmap=         pam    spfuzz=        120
em:     prior=       megap    b=            7500    maxiter=        50
        distance=    1e-05
trim:   wg=             11    ws=              1    endgaps=       yes
data:   n=            1500    N=              30
sample: seed=            0    hsfrac=          0
        searchsize=   1500    norand=         no    csites=       1000
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.294 C 0.231 D 0 E 0 F 0 G 0.257 H 0 I 0 K 0 
L 0 M 0 N 0 P 0 Q 0 R 0 S 0 T 0.217 V 0 
W 0 Y 0 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.291 C 0.229 D 0.000658 E 0.000658 F 0.000658 G 0.255 H 0.000658 I 0.000658 K 0.000658 
L 0.000658 M 0.000658 N 0.000658 P 0.000658 Q 0.000658 R 0.000658 S 0.000658 T 0.215 V 0.000658 
W 0.000658 Y 0.000658 
Background model order: 0
MOTIF GGGGTATAAAA MEME-1	width =  11  sites =  25  llr = 239  E-value = 2.4e-011
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	Motif GGGGTATAAAA MEME-1 Description
	Motif GGGGTATAAAA MEME-1 sites sorted by position p-value
Sequence name             Start   P-value               Site  
-------------             ----- ---------            -----------
chr21_46046964_46047014_     13  1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
	Motif GGGGTATAAAA MEME-1 block diagrams
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
chr21_46046964_46047014_          1.1e-06  12_[1]_27
	Motif GGGGTATAAAA MEME-1 in BLOCKS format
BL   MOTIF GGGGTATAAAA width=11 seqs=25
chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
	Motif GGGGTATAAAA MEME-1 position-specific scoring matrix
log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 
   -32   -680     91     77      7    138    -20     55     64    107     11    150    142     72     87    396   -148    221   -140    -36 
	Motif GGGGTATAAAA MEME-1 position-specific probability matrix
letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 
 0.240000  0.000000  0.000000  0.000000  0.000000  0.680000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.080000  0.000000  0.000000  0.000000 
	Motif GGGGTATAAAA MEME-1 regular expression
[GA][GA][GC][GA]TATA[AT]AA
SUMMARY OF MOTIFS
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
chr21_19617074_19617124_         1.22e-03  39_[1(3.06e-05)]
Stopped because requested number of motifs (1) found.