Mercurial > repos > iuc > meme_meme
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 +-------------------------------------------------------------------------------- \ No newline at end of file