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comparison test-data/meme_output_test1.xml @ 5:f33d77dcacce draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author iuc
date Sat, 09 Apr 2022 08:32:58 +0000
parents 3e5c80594237
children
comparison
equal deleted inserted replaced
4:e383d4bc8682 5:f33d77dcacce
1 <?xml version='1.0' encoding='UTF-8' standalone='yes'?> 1 </motifs>
2 <!-- Document definition --> 2 <scanned_sites_summary p_thresh="0.0001">
3 <!DOCTYPE MEME[ 3 <scanned_sites sequence_id="sequence_0" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="39" pvalue="3.06e-05"/>
4 <!ELEMENT MEME ( 4 </scanned_sites>
5 training_set, 5 <scanned_sites sequence_id="sequence_1" pvalue="2.21e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="27" pvalue="5.52e-05"/>
6 model, 6 </scanned_sites>
7 motifs, 7 <scanned_sites sequence_id="sequence_2" pvalue="7.29e-01" num_sites="0"></scanned_sites>
8 scanned_sites_summary? 8 <scanned_sites sequence_id="sequence_3" pvalue="2.37e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="14" pvalue="5.94e-05"/>
9 )> 9 </scanned_sites>
10 <!ATTLIST MEME
11 version CDATA #REQUIRED
12 release CDATA #REQUIRED
13 <!-- Training-set elements -->
14 <!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>
15 name CDATA #REQUIRED
16 length CDATA #REQUIRED
17 weight CDATA #REQUIRED
18 <!ELEMENT letter_frequencies (alphabet_array)>
19 <!-- Model elements -->
20 <!ELEMENT model (
21 command_line,
22 host,
23 type,
24 nmotifs,
25 )>
26 <!ELEMENT command_line (#PCDATA)*>
27 <!ELEMENT host (#PCDATA)*>
28 <!ELEMENT type (#PCDATA)*>
29 <!ELEMENT nmotifs (#PCDATA)*>
30 <!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->
31 <!ELEMENT left_flank (#PCDATA)>
32 <!-- The site contains the sequence for the motif instance -->
33 <!ELEMENT site (letter_ref*)>
34 <!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->
35 <!ELEMENT right_flank (#PCDATA)>
36 <!-- Scanned site elements -->
37 <!-- Scanned sites are motif occurences found during the sequence scan phase -->
38 <!ELEMENT scanned_sites_summary (scanned_sites*)>
39 <!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>
40 <!ELEMENT scanned_sites (scanned_site*)>
41 <!ATTLIST scanned_sites sequence_id IDREF #REQUIRED
42 pvalue CDATA #REQUIRED
43 num_sites CDATA #REQUIRED>
44 <!ELEMENT scanned_site EMPTY>
45 <!ATTLIST scanned_site motif_id IDREF #REQUIRED
46 strand (plus|minus|none) 'none'
47 position CDATA #REQUIRED
48 pvalue CDATA #REQUIRED>
49 <!-- Utility elements -->
50 <!-- A reference to a letter in the alphabet -->
51 <!ELEMENT letter_ref EMPTY>
52 <!ATTLIST letter_ref letter_id IDREF #REQUIRED>
53 <!-- A alphabet-array contains one floating point value for each letter in an alphabet -->
54 <!ELEMENT alphabet_array (value*)>
55 <!ELEMENT value (#PCDATA)>
56 <!ATTLIST value letter_id IDREF #REQUIRED>
57 <!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->
58 <!ELEMENT alphabet_matrix (alphabet_array*)>
59 ]>
60 <!-- Begin document body -->
61 <MEME version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
62 <alphabet name="Protein" like="protein">
63 <letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
64 </alphabet>
65 <sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
66 <letter_frequencies>
67 <alphabet_array>
68 <value letter_id="A">0.294</value>
69 </letter_frequencies>
70 </training_set>
71 <model>
72 <scores>
73 <alphabet_matrix>
74 <value letter_id="A">-32</value>
75 <value letter_id="A">-79</value>
76 <value letter_id="A">11</value>
77 <value letter_id="A">-596</value>
78 <value letter_id="A">165</value>
79 <value letter_id="A">-838</value>
80 <value letter_id="A">176</value>
81 <value letter_id="A">134</value>
82 <value letter_id="A">165</value>
83 <value letter_id="A">147</value>
84 <value letter_id="A">0.240000</value>
85 <value letter_id="A">0.280000</value>
86 <value letter_id="A">0.160000</value>
87 <value letter_id="A">0.320000</value>
88 <value letter_id="A">0.000000</value>
89 <value letter_id="A">0.960000</value>
90 <value letter_id="A">0.000000</value>
91 <value letter_id="A">1.000000</value>
92 <value letter_id="A">0.760000</value>
93 <value letter_id="A">0.960000</value>
94 <value letter_id="A">0.840000</value>
95 </alphabet_matrix>
96 </probabilities>
97 <regular_expression>
98 [GA][GA][GC][GA]TATA[AT]AA
99 </regular_expression>
100 <contributing_sites>
101 <contributing_site sequence_id="sequence_24" position="12" strand="none" pvalue="1.06e-06" >
102 <left_flank>AAGGCCAGGA</left_flank>
103 <site>
104 <letter_ref letter_id="G"/>
105 </site>
106 <right_flank>GCCTGAGAGC</right_flank>
107 </contributing_site>
108 <contributing_site sequence_id="sequence_25" position="36" strand="none" pvalue="3.41e-06" >
109 <left_flank>ACAGGCCCTG</left_flank>
110 <right_flank>GCC</right_flank>
111 </contributing_site>
112 <contributing_site sequence_id="sequence_19" position="9" strand="none" pvalue="3.41e-06" >
113 <left_flank>CAGGCCCTG</left_flank>
114 <right_flank>GCCCCAGCAG</right_flank>
115 <scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="3.06e-05"/> 10 <scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="3.06e-05"/>
11 </scanned_sites>
116 <scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/> 12 <scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/>
13 </scanned_sites>
117 <scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/> 14 <scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/>
15 </scanned_sites>
16 <scanned_sites sequence_id="sequence_7" pvalue="1.81e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="4.54e-05"/>
17 </scanned_sites>
18 <scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites>
19 <scanned_sites sequence_id="sequence_9" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="3.41e-06"/>
20 </scanned_sites>
21 <scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites>
22 <scanned_sites sequence_id="sequence_11" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="16" pvalue="8.67e-06"/>
23 </scanned_sites>
24 <scanned_sites sequence_id="sequence_12" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="18" pvalue="8.67e-06"/>
25 </scanned_sites>
26 <scanned_sites sequence_id="sequence_13" pvalue="2.01e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="5.01e-06"/>
27 </scanned_sites>
28 <scanned_sites sequence_id="sequence_14" pvalue="8.11e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="19" pvalue="2.03e-05"/>
29 </scanned_sites>
30 <scanned_sites sequence_id="sequence_15" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="21" pvalue="8.67e-06"/>
31 </scanned_sites>
32 <scanned_sites sequence_id="sequence_16" pvalue="2.71e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="22" pvalue="6.78e-05"/>
33 </scanned_sites>
34 <scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites>
35 <scanned_sites sequence_id="sequence_18" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="37" pvalue="3.82e-05"/>
36 </scanned_sites>
37 <scanned_sites sequence_id="sequence_19" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="9" pvalue="3.41e-06"/>
38 </scanned_sites>
39 <scanned_sites sequence_id="sequence_20" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="1.59e-05"/>
40 </scanned_sites>
41 <scanned_sites sequence_id="sequence_21" pvalue="1.60e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="7" pvalue="4.00e-06"/>
42 </scanned_sites>
43 <scanned_sites sequence_id="sequence_22" pvalue="4.83e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="2" pvalue="1.21e-05"/>
44 </scanned_sites>
45 <scanned_sites sequence_id="sequence_23" pvalue="2.43e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="6.06e-06"/>
46 </scanned_sites>
47 <scanned_sites sequence_id="sequence_24" pvalue="4.26e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="1.06e-06"/>
48 </scanned_sites>
49 <scanned_sites sequence_id="sequence_25" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="36" pvalue="3.41e-06"/>
50 </scanned_sites>
51 <scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites>
52 <scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites>
53 <scanned_sites sequence_id="sequence_28" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="1.59e-05"/>
54 </scanned_sites>
55 <scanned_sites sequence_id="sequence_29" pvalue="1.61e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="30" pvalue="4.02e-05"/>
56 </scanned_sites>
57 </scanned_sites_summary>
118 </MEME> 58 </MEME>