Mercurial > repos > iuc > meme_dreme

diff test-data/dreme1.txt @ 0:b386032d758d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author: iuc
date: Wed, 25 Apr 2018 12:13:22 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dreme1.txt	Wed Apr 25 12:13:22 2018 -0400
@@ -0,0 +1,102 @@
+# DREME 4.12.0
+#     command: dreme -oc dreme_out -rna -norc -p dreme_test_sites.fa -e 0.05 -mink 3 -maxk 8
+#   positives: 1000 from dreme_test_sites.fa (Thu Apr 19 19:09:45 CEST 2018)
+#   negatives: 1000 from shuffled positives
+#        host: ThinkPad-T450s
+#        when: Thu Apr 19 19:11:17 CEST 2018
+
+MEME version 4.12.0
+
+ALPHABET "RNA" RNA-LIKE
+A "Adenine" CC0000
+C "Cytosine" 0000CC
+G "Guanine" FFB300
+U "Uracil" 008000
+N "Any base" = ACGU
+X = ACGU
+. = ACGU
+V "Not U" = ACG
+H "Not G" = ACU
+D "Not C" = AGU
+B "Not A" = CGU
+M "Amino" = AC
+R "Purine" = AG
+W "Weak" = AU
+S "Strong" = CG
+Y "Pyrimidine" = CU
+K "Keto" = GU
+T = U
+END ALPHABET
+
+Background letter frequencies (from dataset):
+A 0.221 C 0.245 G 0.221 U 0.312
+
+
+MOTIF UUYUCY DREME-1
+
+#             Word        Pos        Neg    P-value    E-value
+# BEST      UUYUCY        387        210   2.6e-018   1.2e-013
+#           UUUUCC        147         75   1.8e-007   8.1e-003
+#           UUUUCU        155         94   2.2e-005   1.0e+000
+#           UUCUCU         94         51   1.3e-004   6.1e+000
+#           UUCUCC         75         42   1.1e-003   5.0e+001
+
+letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013
+0.000000 0.000000 0.000000 1.000000
+0.000000 0.000000 0.000000 1.000000
+0.000000 0.294118 0.000000 0.705882
+0.000000 0.000000 0.000000 1.000000
+0.000000 1.000000 0.000000 0.000000
+0.000000 0.474946 0.000000 0.525054
+
+
+MOTIF YAGG DREME-2
+
+#             Word        Pos        Neg    P-value    E-value
+# BEST        YAGG        600        416   1.1e-016   5.1e-012
+#             CAGG        441        304   1.5e-010   6.6e-006
+#             UAGG        232        165   1.1e-004   4.7e+000
+
+letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012
+0.000000 0.692308 0.000000 0.307692
+1.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 1.000000 0.000000
+0.000000 0.000000 1.000000 0.000000
+
+
+MOTIF GAAGAW DREME-3
+
+#             Word        Pos        Neg    P-value    E-value
+# BEST      GAAGAW         81         22   8.2e-010   3.4e-005
+#           GAAGAU         45          7   2.4e-008   9.9e-004
+#           GAAGAA         40         16   7.9e-004   3.3e+001
+
+letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005
+0.000000 0.000000 1.000000 0.000000
+1.000000 0.000000 0.000000 0.000000
+1.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 1.000000 0.000000
+1.000000 0.000000 0.000000 0.000000
+0.494382 0.000000 0.000000 0.505618
+
+
+MOTIF SMUGGA DREME-4
+
+#             Word        Pos        Neg    P-value    E-value
+# BEST      SMUGGA        110         47   9.1e-008   3.7e-003
+#           GAUGGA         22          6   1.7e-003   7.1e+001
+#           GCUGGA         33         14   3.6e-003   1.5e+002
+#           CCUGGA         32         15   8.6e-003   3.5e+002
+#           CAUGGA         29         13   9.1e-003   3.7e+002
+
+letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003
+0.000000 0.529412 0.470588 0.000000
+0.428571 0.571429 0.000000 0.000000
+0.000000 0.000000 0.000000 1.000000
+0.000000 0.000000 1.000000 0.000000
+0.000000 0.000000 1.000000 0.000000
+1.000000 0.000000 0.000000 0.000000
+
+
+# Stopping reason: E-value threshold exceeded
+#    Running time: 13.45 seconds