Mercurial > repos > jjkoehorst > sapp
diff rnaseq/cutadapt/test-data/meme/fimo/fimo_output_xml_1.xml @ 11:a712b378e090
cutadapt added
author | jjkoehorst <jasperkoehorst@gmail.com> |
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date | Sat, 21 Feb 2015 16:33:42 +0100 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaseq/cutadapt/test-data/meme/fimo/fimo_output_xml_1.xml Sat Feb 21 16:33:42 2015 +0100 @@ -0,0 +1,53 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<?xml-stylesheet type="text/xsl" href="fimo-to-html.xsl"?> +<!-- Begin document body --> +<fimo version="4.6.0" release="8 PST 20"> + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" +> +<command-line>fimo --o /path/to/dataset_?_files --verbosity 1 /path/to/dataset_?.dat /path/to/dataset_?.dat</command-line> +<settings> +<setting name="output directory">/path/to/dataset_?_files</setting> +<setting name="MEME file name">/path/to/dataset_?.dat</setting> +<setting name="sequence file name">/path/to/dataset_?.dat</setting> +<setting name="background file name">(null)</setting> +<setting name="motif name">motif</setting> +<setting name="allow clobber">false</setting> +<setting name="compute q-values">true</setting> +<setting name="output p-threshold set">false</setting> +<setting name="output q-threshold set">false</setting> +<setting name="text only">false</setting> +<setting name="scan both strands">false</setting> +<setting name="max sequence length">250000000</setting> +<setting name="output q-value threshold"> 1</setting> +<setting name="output p-value threshold">0.0001</setting> +<setting name="pseudocount">0.1</setting> +<setting name="verbosity">1</setting> +</settings> +<sequence-data num-sequences="1" num-residues="5386" /> +<alphabet>protein</alphabet> +<motif name="1" width="11" best-possible-match="GGGGTATAAAA"/> +<background source="non-redundant database"> +<value letter="A">0.073</value> +<value letter="C">0.018</value> +<value letter="D">0.052</value> +<value letter="E">0.062</value> +<value letter="F">0.040</value> +<value letter="G">0.069</value> +<value letter="H">0.022</value> +<value letter="I">0.056</value> +<value letter="K">0.058</value> +<value letter="L">0.092</value> +<value letter="M">0.023</value> +<value letter="N">0.046</value> +<value letter="P">0.051</value> +<value letter="Q">0.041</value> +<value letter="R">0.052</value> +<value letter="S">0.074</value> +<value letter="T">0.059</value> +<value letter="V">0.064</value> +<value letter="W">0.013</value> +<value letter="Y">0.033</value> +</background> +<cisml-file>cisml.xml</cisml-file> +</fimo>