Mercurial > repos > iuc > meme_psp_gen

diff test-data/meme_output_test1.txt @ 6:5f95d385a33c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author iuc
date Sat, 09 Apr 2022 08:33:29 +0000
parents ff2f53a32d0e
children
line wrap: on
line diff
--- a/test-data/meme_output_test1.txt	Sat Nov 27 14:38:09 2021 +0000
+++ b/test-data/meme_output_test1.txt	Sat Apr 09 08:33:29 2022 +0000
@@ -1,61 +1,39 @@
 ********************************************************************************
-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
+SUMMARY OF MOTIFS
+********************************************************************************
+
 --------------------------------------------------------------------------------
-	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.
+chr21_26934381_26934431_         2.21e-03  27_[1(5.52e-05)]_12
+chr21_28217753_28217803_         7.29e-01  50
+chr21_31710037_31710087_         2.37e-03  14_[1(5.94e-05)]_25
+chr21_31744582_31744632_         1.22e-03  12_[1(3.06e-05)]_27
+chr21_31768316_31768366_         1.53e-03  [1(3.82e-05)]_39
+chr21_31914206_31914256_         6.70e-04  15_[1(1.68e-05)]_24
+chr21_31933633_31933683_         1.81e-03  4_[1(4.54e-05)]_35
+chr21_31962741_31962791_         1.61e-02  50
+chr21_31964683_31964733_         1.36e-04  13_[1(3.41e-06)]_26
+chr21_31973364_31973414_         1.99e-01  50
+chr21_31992870_31992920_         3.47e-04  16_[1(8.67e-06)]_23
+chr21_32185595_32185645_         3.47e-04  18_[1(8.67e-06)]_21
+chr21_32202076_32202126_         2.01e-04  13_[1(5.01e-06)]_26
+chr21_32253899_32253949_         8.11e-04  19_[1(2.03e-05)]_20
+chr21_32410820_32410870_         3.47e-04  21_[1(8.67e-06)]_18
+chr21_36411748_36411798_         2.71e-03  22_[1(6.78e-05)]_17
+chr21_37838750_37838800_         8.23e-02  50
+chr21_45705687_45705737_         1.53e-03  37_[1(3.82e-05)]_2
+chr21_45971413_45971463_         1.36e-04  9_[1(3.41e-06)]_30
+chr21_45978668_45978718_         6.37e-04  4_[1(1.59e-05)]_35
+chr21_45993530_45993580_         1.60e-04  7_[1(4.00e-06)]_32
+chr21_46020421_46020471_         4.83e-04  2_[1(1.21e-05)]_37
+chr21_46031920_46031970_         2.43e-04  15_[1(6.06e-06)]_24
+chr21_46046964_46047014_         4.26e-05  12_[1(1.06e-06)]_27
+chr21_46057197_46057247_         1.36e-04  36_[1(3.41e-06)]_3
+chr21_46086869_46086919_         4.30e-02  50
+chr21_46102103_46102153_         4.30e-02  50
+chr21_47517957_47518007_         6.37e-04  32_[1(1.59e-05)]_7
+chr21_47575506_47575556_         1.61e-03  30_[1(4.02e-05)]_9