Mercurial > repos > iuc > meme_meme

comparison test-data/meme_output_test2.xml @ 18:19237efe98d1 draft

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 08:34:02 +0000
parents 3f0dd362b755
children
comparison
equal deleted inserted replaced
17:e7242484929c 18:19237efe98d1
1 <?xml version='1.0' encoding='UTF-8' standalone='yes'?> 1 </motifs>
2 <!-- Document definition -->
3 <!DOCTYPE MEME[
4 <!ELEMENT MEME (
5 training_set,
6 model,
7 motifs,
8 scanned_sites_summary?
9 )>
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 <!ATTLIST training_set primary_sequences CDATA #REQUIRED primary_count CDATA #REQUIRED primary_positions CDATA #REQUIRED
16 control_sequences CDATA "" control_count CDATA "" control_positions CDATA "">
17 <!ELEMENT alphabet (letter*)>
18 <!ATTLIST alphabet name CDATA #REQUIRED>
19 <!ELEMENT letter_frequencies (alphabet_array)>
20 <!-- Model elements -->
21 <!ELEMENT model (
22 command_line,
23 host,
24 type,
25 nmotifs,
26 )>
27 <!ELEMENT command_line (#PCDATA)*>
28 <!ELEMENT motifs (motif*)>
29 <!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>
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 <training_set primary_sequences="Galaxy_FASTA_Input" primary_count="30" primary_positions="1500" control_sequences="--none--" control_count="0" control_positions="0">
40 <alphabet name="DNA" like="dna">
41 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
42 <sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
43 <value letter_id="G">0.257</value>
44 <value letter_id="T">0.217</value>
45 </alphabet_array>
46 <model>
47 <type>zoops</type>
48 <scores>
49 <alphabet_matrix>
50 <alphabet_array>
51 <value letter_id="A">-14</value>
52 <value letter_id="A">3</value>
53 <value letter_id="A">-1155</value>
54 <value letter_id="A">156</value>
55 <value letter_id="A">-1155</value>
56 <value letter_id="A">172</value>
57 <value letter_id="A">125</value>
58 <value letter_id="A">167</value>
59 <value letter_id="A">144</value>
60 <value letter_id="A">0.266667</value>
61 <value letter_id="A">0.300000</value>
62 <value letter_id="A">0.800000</value>
63 <contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" >
64 <left_flank>AAGGCCAGGA</left_flank>
65 <letter_ref letter_id="G"/>
66 <right_flank>GCCTGAGAGC</right_flank>
67 <contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" >
68 <letter_ref letter_id="A"/>
69 <contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >
70 <right_flank>AGCCCTGTAC</right_flank>
71 <contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >
72 <left_flank>CGTGGTCGCG</left_flank>
73 <right_flank>GC</right_flank>
74 <contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" >
75 <left_flank>GCTGCCGGTG</left_flank>
76 <right_flank>GCCCTGGCG</right_flank>
77 <contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" >
78 <scanned_sites_summary p_thresh="0.0001"> 2 <scanned_sites_summary p_thresh="0.0001">
79 <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/> 3 <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/>
4 </scanned_sites>
80 <scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/> 5 <scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/>
6 </scanned_sites>
81 <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites> 7 <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>
8 <scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/>
9 </scanned_sites>
10 <scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.04e-05"/>
11 </scanned_sites>
12 <scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>
13 </scanned_sites>
14 <scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>
15 </scanned_sites>
16 <scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>
17 </scanned_sites>
18 <scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>
19 <scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>
20 </scanned_sites>
21 <scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>
22 <scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>
23 </scanned_sites>
24 <scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>
25 </scanned_sites>
26 <scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>
27 </scanned_sites>
28 <scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>
29 </scanned_sites>
30 <scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>
31 </scanned_sites>
32 <scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>
33 </scanned_sites>
34 <scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>
35 <scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>
36 </scanned_sites>
37 <scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>
38 </scanned_sites>
39 <scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>
40 </scanned_sites>
41 <scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>
42 </scanned_sites>
43 <scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>
44 </scanned_sites>
45 <scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>
46 </scanned_sites>
47 <scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>
48 </scanned_sites>
49 <scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>
50 </scanned_sites>
51 <scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>
52 <scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>
53 <scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>
54 </scanned_sites>
55 <scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>
56 </scanned_sites>
57 </scanned_sites_summary>
82 </MEME> 58 </MEME>