diff test-data/meme_output_test2.txt @ 18:19237efe98d1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author iuc
date Sat, 09 Apr 2022 08:34:02 +0000
parents 3f0dd362b755
children
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--- a/test-data/meme_output_test2.txt	Sat Nov 27 14:38:35 2021 +0000
+++ b/test-data/meme_output_test2.txt	Sat Apr 09 08:34:02 2022 +0000
@@ -1,86 +1,40 @@
 ********************************************************************************
-MEME - Motif discovery tool
-MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)
-REFERENCE
-TRAINING SET
-PRIMARY SEQUENCES= Galaxy_FASTA_Input
-CONTROL SEQUENCES= --none--
-ALPHABET= ACGT
-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
-strands: +
-width:  minw=            8    maxw=           50
-nsites: minsites=        2    maxsites=       30    wnsites=       0.8
-theta:  spmap=         uni    spfuzz=        0.5
-em:     prior=   dirichlet    b=            0.01    maxiter=        50
-        distance=    0.001
-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:
-Letter frequencies in dataset:
-A 0.294 C 0.231 G 0.257 T 0.217 
-Background letter frequencies (from file dataset with add-one prior applied):
-A 0.294 C 0.231 G 0.257 T 0.217 
-Background model order: 0
-MOTIF GGSRTATAAAA MEME-1	width =  11  sites =  30  llr = 254  E-value = 5.1e-040
-	Motif GGSRTATAAAA MEME-1 Description
-Simplified        A  3313:9:a798
-pos.-specific     C  1:3::1:::1:
-probability       G  6756::::::2
-matrix            T  1:11a1a:3::
+SUMMARY OF MOTIFS
+********************************************************************************
 
-         bits    2.2       *    
-                 2.0     * *    
-                 1.8     * *    
-                 1.5     * ** * 
-Relative         1.3     * ** * 
-Entropy          1.1     ****** 
-(12.2 bits)      0.9  *  *******
-                 0.7  *  *******
-                 0.4 ** ********
-                 0.2 ***********
-                 0.0 -----------
-
-Multilevel           GGGGTATAAAA
-consensus            AACA    T  
-sequence                        
-	Motif GGSRTATAAAA MEME-1 sites sorted by position p-value
-Sequence name             Start   P-value               Site  
-chr21_46046964_46047014_     13  4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
-	Motif GGSRTATAAAA MEME-1 block diagrams
-SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
+--------------------------------------------------------------------------------
+	Combined block diagrams: non-overlapping sites with p-value < 0.0001
+--------------------------------------------------------------------------------
+SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 -------------            ----------------  -------------
-chr21_46046964_46047014_          4.5e-07  12_[+1]_27
-	Motif GGSRTATAAAA MEME-1 in BLOCKS format
-BL   MOTIF GGSRTATAAAA width=11 seqs=30
-chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
-	Motif GGSRTATAAAA MEME-1 position-specific scoring matrix
-log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 
-   -14   -179    114   -112 
-     3  -1155    137   -270 
-  -114     20     86    -71 
-     3   -279    122   -170 
- -1155  -1155   -295    215 
-   156   -179  -1155   -170 
- -1155  -1155  -1155    220 
-   172   -279  -1155  -1155 
-   125  -1155  -1155     46 
-   167   -179  -1155  -1155 
-   144  -1155    -63   -270 
-	Motif GGSRTATAAAA MEME-1 position-specific probability matrix
-letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 
- 0.266667  0.066667  0.566667  0.100000 
-	Motif GGSRTATAAAA 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_         5.63e-04  39_[+1(1.41e-05)]
-Stopped because requested number of motifs (1) found.
+chr21_26934381_26934431_         1.57e-03  27_[+1(3.93e-05)]_12
+chr21_28217753_28217803_         1.00e-01  50
+chr21_31710037_31710087_         2.49e-03  14_[+1(6.24e-05)]_25
+chr21_31744582_31744632_         1.22e-03  12_[+1(3.04e-05)]_27
+chr21_31768316_31768366_         1.47e-03  [+1(3.67e-05)]_39
+chr21_31914206_31914256_         6.45e-04  15_[+1(1.61e-05)]_24
+chr21_31933633_31933683_         2.26e-03  4_[+1(5.65e-05)]_35
+chr21_31962741_31962791_         3.37e-02  50
+chr21_31964683_31964733_         1.95e-04  13_[+1(4.86e-06)]_26
+chr21_31973364_31973414_         5.73e-02  50
+chr21_31992870_31992920_         5.52e-04  16_[+1(1.38e-05)]_23
+chr21_32185595_32185645_         2.59e-04  18_[+1(6.48e-06)]_21
+chr21_32202076_32202126_         1.10e-04  13_[+1(2.74e-06)]_26
+chr21_32253899_32253949_         7.78e-04  17_[+1(1.95e-05)]_22
+chr21_32410820_32410870_         5.52e-04  21_[+1(1.38e-05)]_18
+chr21_36411748_36411798_         2.85e-03  22_[+1(7.15e-05)]_17
+chr21_37838750_37838800_         1.90e-02  50
+chr21_45705687_45705737_         8.63e-04  37_[+1(2.16e-05)]_2
+chr21_45971413_45971463_         1.95e-04  9_[+1(4.86e-06)]_30
+chr21_45978668_45978718_         2.59e-04  4_[+1(6.48e-06)]_35
+chr21_45993530_45993580_         1.95e-04  7_[+1(4.86e-06)]_32
+chr21_46020421_46020471_         7.78e-04  2_[+1(1.95e-05)]_37
+chr21_46031920_46031970_         8.89e-05  15_[+1(2.22e-06)]_24
+chr21_46046964_46047014_         1.80e-05  12_[+1(4.51e-07)]_27
+chr21_46057197_46057247_         1.95e-04  36_[+1(4.86e-06)]_3
+chr21_46086869_46086919_         5.54e-03  50
+chr21_46102103_46102153_         5.54e-03  50
+chr21_47517957_47518007_         2.59e-04  32_[+1(6.48e-06)]_7
+chr21_47575506_47575556_         1.22e-03  30_[+1(3.04e-05)]_9
+--------------------------------------------------------------------------------
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