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diff tools/mytools/fimo_out/fimo-to-html.xsl @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mytools/fimo_out/fimo-to-html.xsl Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,761 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<xsl:stylesheet version="1.0" + xmlns:xsl="http://www.w3.org/1999/XSL/Transform" + xmlns:cis="http://zlab.bu.edu/schema/cisml" + xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" + xmlns:mem="http://noble.gs.washington.edu/meme" +> + + <xsl:output method="html" indent="yes" + doctype-public="-//W3C//DTD HTML 4.01 Transitional//EN" + doctype-system="http://www.w3.org/TR/html4/loose.dtd" + /> + + <!-- Stylesheet processing starts here --> + <xsl:template match="/fimo"> + <html> + <xsl:call-template name="html_head"/> + <body bgcolor='#D5F0FF'> + <a name="top_buttons"></a> + <hr /> + <table summary="buttons" align="left" cellspacing="0"> + <tr> + <td bgcolor="#00FFFF"> + <a href='#database_and_motifs'><b>Database and Motifs</b></a> + </td> + <td bgcolor="#DDFFDD"> + <a href="#sec_i"><b>High-scoring Motif Occurences</b></a> + </td> + <td bgcolor="#DDDDFF"> + <a href="#debugging_information"><b>Debugging Information</b></a> + </td> + </tr> + </table> + <br /> + <br /> + <!-- Create the various sub-sections of the document --> + <xsl:call-template name="version"/> + <xsl:call-template name="database_and_motifs"/> + <xsl:call-template name="high_scoring_motif_occurrences"/> + <!-- Diagrams and annotations break for long sequences + (H. sap. chr21 for example --> + <!-- + <xsl:call-template name="motif_diagrams"/> + <xsl:call-template name="annotations"/> + --> + <xsl:call-template name="debugging_information"/> + <!-- Buttons are pointless since there is only one section + <xsl:call-template name="button_help"/> + --> + </body> + </html> + </xsl:template> + + <xsl:template name="html_head"> + <!-- This template prints the HTML head block, including the document level CSS. --> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/> + <title>FIMO Results</title> + <style type="text/css"> + td.left {text-align: left;} + td.right {text-align: right; padding-right: 1cm;} + </style> + </head> + </xsl:template> + + <xsl:template name="version"> + <!-- + This template prints the HTML describing the version of FIMO + that generated this document. + --> + <hr /> + <center> + <big><b>FIMO - Motif search tool</b></big> + </center> + <hr /> + <p> + FIMO version <xsl:value-of select="@version"/>, + (Release date: <xsl:value-of select="@release"/>) + </p> + <p> + For further information on how to interpret these results + or to get a copy of the FIMO software please access + <a href="http://meme.nbcr.net">http://meme.nbcr.net</a> + </p> + <p>If you use FIMO in your research, please cite the following paper:<br /> + Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, + "FIMO: Scanning for occurrences of a given motif", + <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011. + </p> + </xsl:template> + + <xsl:template name="reference"> + <!-- This template prints the instructions for citing FIMO. --> + <hr/> + <center> + <a name="reference"/> + <big><b>REFERENCE</b></big> + </center> + <hr/> + <p> + If you use this program in your research, please cite: + </p> + <p> + </p> + </xsl:template> + + <xsl:template name="database_and_motifs"> + <!-- + This template prints the HTML descibing the input sequences + and motifs that were used to generate this document. + --> + <hr/> + <center> + <big> + <b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b> + </big> + </center> + <hr/> + <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;"> + <p> + DATABASE + <xsl:value-of select="/fimo/settings/setting[@name='sequence file name']"/> + <br /> + Database contains + <xsl:value-of select="/fimo/sequence-data/@num-sequences"/> + sequences, + <xsl:value-of select="/fimo/sequence-data/@num-residues"/> + residues + </p> + <p> + MOTIFS + <xsl:value-of select="/fimo/settings/setting[@name='MEME file name']"/> + <xsl:text> </xsl:text> + (<xsl:value-of select="/fimo/alphabet"/>) + <table> + <thead> + <tr> + <th style="border-bottom: 1px dashed;">MOTIF</th> + <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th> + <th style="border-bottom: 1px dashed; padding-left: 1em;" align="left"> + BEST POSSIBLE MATCH + </th> + </tr> + </thead> + <tbody> + <xsl:for-each select="/fimo/motif"> + <tr> + <td align="right"><xsl:value-of select="./@name"/></td> + <td align="right" style="padding-left: 1em;"><xsl:value-of select="./@width"/></td> + <td align="left" style="padding-left: 1em;"> + <xsl:value-of select="./@best-possible-match"/> + </td> + </tr> + </xsl:for-each> + </tbody> + </table> + </p> + <p> + Random model letter frequencies + (from <xsl:value-of select="/fimo/background/@source"/>): + <br /> + <xsl:call-template name="bg_freq"/> + </p> + </div> + </xsl:template> + + <xsl:template name="bg_freq"> + <!-- This template prints the HTML listing the background frequencies for each symbol in the alphabet. --> + <xsl:for-each select="/fimo/background/value"> + <xsl:value-of select="./@letter"/> + <xsl:text> </xsl:text> + <xsl:value-of select="format-number(., '0.000')"/> + <xsl:text> </xsl:text> + <!-- For amino acids insert a line break very 9 characters. --> + <xsl:variable name="letter_index" select="position()" /> + <xsl:if test="$letter_index mod 9 = 0"> + <xsl:text> </xsl:text> + <br/> + <xsl:text> </xsl:text> + </xsl:if> + </xsl:for-each> + </xsl:template> + + <xsl:template name="high_scoring_motif_occurrences"> + <xsl:variable name="alphabet"> + <xsl:value-of select="/fimo/alphabet"/> + </xsl:variable> + <xsl:variable name="num_qvalues"> + <xsl:value-of + select="count(document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/cis:matched-element/mem:qvalue)"/> + </xsl:variable> + <!-- This template prints the matches to the pattern. --> + <hr/> + <center> + <big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big> + </center> + <hr/> + <ul> + <li> Each of the following + <xsl:value-of select="count(document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/cis:matched-element)"/> + motif occurrences has + <xsl:choose> + <xsl:when test="/fimo/settings/setting[@name='output q-threshold set'] = 'true'"> + q-value less than + <xsl:value-of select="/fimo/settings/setting[@name='output q-value threshold' = 'true']"/> + </xsl:when> + <xsl:otherwise> + p-value less than + <xsl:value-of select="/fimo/settings/setting[@name='output p-value threshold']"/> + </xsl:otherwise> + </xsl:choose> + </li> + <li> The p-value of a motif occurrence is defined as the + probability of a random sequence of the same length as the motif + matching that position of the sequence with as good or better a score. + </li> + <li> The score for the match of a position in a sequence to a motif + is computed by summing the appropriate entries from each column of + the position-dependent scoring matrix that represents the motif. + </li> + <xsl:if test="$num_qvalues > 0"> + <li> The q-value of a motif occurrence is defined as the + false discovery rate if the occurrence is accepted as significant. + </li> + </xsl:if> + <li>The table is sorted by increasing p-value.</li> + <li>If the start position is larger than the end position, + the motif occurrence is on the reverse strand. + </li> + </ul> + <table border="1"> + <thead> + <tr> + <th>Motif</th> + <th>Sequence Name</th> + <xsl:if test="$alphabet='nucleotide'"> + <th>Strand</th> + </xsl:if> + <th>Start</th> + <th>End</th> + <th>p-value</th> + <xsl:if test="$num_qvalues > 0"> + <th>q-value</th> + </xsl:if> + <th>Matched Sequence</th> + </tr> + </thead> + <tbody> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/cis:matched-element"> + <xsl:sort select="@pvalue" data-type="number" order="ascending"/> + <xsl:variable name="seq_name" select="../@name"/> + <tr> + <td align="left"> + <a name="occurrences_{$seq_name}"><xsl:value-of select="../../@name"/></a> + </td> + <td align="left"> + <xsl:value-of select="../@name"/> + </td> + <!-- start and stop positions --> + <!-- CISML uses start > stop to indicate - strand --> + <!-- For HTML we want start < stop, indicate strand in strand column --> + <xsl:if test="$alphabet='nucleotide'"> + <xsl:choose> + <xsl:when test="@start > @stop"> + <!-- start > stop so - strand --> + <td align="center"><xsl:text>−</xsl:text></td> + </xsl:when> + <xsl:otherwise> + <td align="center"><xsl:text>+</xsl:text></td> + </xsl:otherwise> + </xsl:choose> + </xsl:if> + <xsl:choose> + <xsl:when test="@start > @stop"> + <!-- start > stop so - strand --> + <td align="left"> + <xsl:value-of select="@stop"/> + </td> + <td align="left"> + <xsl:value-of select="@start"/> + </td> + </xsl:when> + <xsl:otherwise> + <td align="left"> + <xsl:value-of select="@start"/> + </td> + <td align="left"> + <xsl:value-of select="@stop"/> + </td> + </xsl:otherwise> + </xsl:choose> + <td align="left"> + <xsl:value-of select="@pvalue"/> + </td> + <xsl:if test="$num_qvalues > 0"> + <td align="left"> + <xsl:value-of select="./mem:qvalue"/> + </td> + </xsl:if> + <td align="left"> + <code style="font-size: x-large;"><xsl:value-of select="./cis:sequence"/></code> + </td> + </tr> + </xsl:for-each> + </tbody> + </table> + </xsl:template> + + <xsl:template name="motif_diagrams"> + <!-- + This template draws the bead-on-string diagram for each + of the scanned sequence. + --> + <hr/> + <center> + <big><b><a name="sec_ii">SECTION II: MOTIF DIAGRAMS</a></b></big> + </center> + <hr/> + <table border="1"> + <thead> + <tr> + <th align="left"><br/>Name</th> + <th align="left"><br/>Motifs</th> + <th></th> + </tr> + </thead> + <tbody> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[not (@name = preceding::cis:scanned-sequence/@name)]"> + <xsl:sort select="@name" order="ascending"/> + <xsl:variable name="sequence_width" select="@length"/> + <xsl:variable name="sequence_name" select="@name"/> + <tr> + <td><a name="diagram_{$sequence_name}"><xsl:value-of select="$sequence_name"/></a></td> + <td> + <table> + <tr> + <xsl:call-template name="draw_diagram_for_sequence"> + <xsl:with-param name="sequence_name" select="$sequence_name"/> + <xsl:with-param name="sequence_width" select="@length"/> + </xsl:call-template> + </tr> + </table> + </td> + </tr> + </xsl:for-each> + <tr> + <td rowspan="2" style="color: blue;">SCALE</td> + <td> + <table> + <tr> + <td> + <xsl:call-template name="ticks"> + <xsl:with-param name="count" select="1"/> + <xsl:with-param name="limit"> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/@length"> + <xsl:sort data-type="number" order="descending"/> + <xsl:if test="position()=1"><xsl:value-of select="."/></xsl:if> + </xsl:for-each> + </xsl:with-param> + </xsl:call-template> + </td> + </tr> + <tr> + <td> + <xsl:call-template name="scale"> + <xsl:with-param name="count" select="1"/> + <xsl:with-param name="limit"> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence/@length"> + <xsl:sort data-type="number" order="descending"/> + <xsl:if test="position()=1"><xsl:value-of select="."/></xsl:if> + </xsl:for-each> + </xsl:with-param> + </xsl:call-template> + </td> + </tr> + </table> + </td> + </tr> + </tbody> + </table> + </xsl:template> + + <xsl:template name="draw_diagram_for_sequence"> + <!-- + This template draws the bead-on-string diagram for + a single sequence. + --> + <xsl:param name="sequence_name"/> + <xsl:param name="sequence_width"/> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name = $sequence_name]/cis:matched-element"> + <xsl:sort select="number(@start)" data-type="number" order="ascending"/> + <xsl:variable name="starting"> + <xsl:choose> + <xsl:when test="number(@start) < number(@stop)"> + <xsl:value-of select="@start"/> + </xsl:when> + <xsl:otherwise> + <xsl:value-of select="@stop"/> + </xsl:otherwise> + </xsl:choose> + </xsl:variable> + <xsl:variable name="ending"> + <xsl:choose> + <xsl:when test="number(@start) < number(@stop)"> + <xsl:value-of select="@stop"/> + </xsl:when> + <xsl:otherwise> + <xsl:value-of select="@start"/> + </xsl:otherwise> + </xsl:choose> + </xsl:variable> + <xsl:variable name="current_element" select="position()"/> + <xsl:variable name="previous_end"> + <xsl:choose> + <xsl:when test="position() = 1">0</xsl:when> + <xsl:otherwise> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name = $sequence_name]/cis:matched-element"> + <xsl:sort select="number(@start)" data-type="number" order="ascending"/> + <xsl:if test="position() = ($current_element - 1)"> + <xsl:choose> + <xsl:when test="number(@start) < number(@stop)"> + <xsl:value-of select="@stop"/> + </xsl:when> + <xsl:otherwise> + <xsl:value-of select="@start"/> + </xsl:otherwise> + </xsl:choose> + </xsl:if> + </xsl:for-each> + </xsl:otherwise> + </xsl:choose> + </xsl:variable> + <xsl:variable name="motif_name"> + <xsl:value-of select="../../@name"/> + </xsl:variable> + <xsl:variable name="motif_index"> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern"> + <xsl:if test="@name = $motif_name"><xsl:value-of select="position()"/></xsl:if> + </xsl:for-each> + <xsl:value-of select="@name"/> + </xsl:variable> + <xsl:variable name="motif_color"> + <xsl:call-template name="pick_color"> + <xsl:with-param name="index" select="$motif_index"/> + </xsl:call-template> + </xsl:variable> + <xsl:variable name="font_color"> + <xsl:call-template name="pick_font_color"> + <xsl:with-param name="index" select="$motif_index"/> + </xsl:call-template> + </xsl:variable> + <xsl:variable name="strand"> + <xsl:choose> + <xsl:when test="number(@start) < number(@stop)"> + <xsl:text>+</xsl:text> + </xsl:when> + <xsl:otherwise> + <xsl:text>-</xsl:text> + </xsl:otherwise> + </xsl:choose> + </xsl:variable> + <xsl:variable name="alphabet" select="document('fimo.xml')/fimo/alphabet"/> + <td style="width: {2 * ($starting - $previous_end) }px;"><hr size="4" noshade="noshade"/></td> + <td style="width: {2 * ($ending - $starting)}px; background: {$motif_color}; color: {$font_color}; text-align: center;"> + <xsl:if test="$alphabet = 'nucleotide'"><xsl:value-of select="$strand"/></xsl:if> + <xsl:value-of select="../../@name"/> + </td> + <xsl:if test="position() = last()"> + <td style="width: {2 * ($sequence_width - $ending) }px;"><hr size="4" noshade="noshade"/></td> + </xsl:if> + </xsl:for-each> + </xsl:template> + + <xsl:template name="ticks"> + <!-- + This template is used to print the tick marks in the + scale at the bottom of the bead-on-string daigrams. + --> + <xsl:param name="count" select="1"/> + <xsl:param name="limit" select="1"/> + <xsl:if test="$count < $limit"> + <td style="width: 50px;" align="left"><font color="blue">|</font></td> + <xsl:call-template name="ticks"> + <xsl:with-param name="count" select="$count + 24"/> + <xsl:with-param name="limit" select="$limit"/> + </xsl:call-template> + </xsl:if> + </xsl:template> + + <xsl:template name="scale"> + <!-- + This template is used to print the text in the + scale at the bottom of the bead-on-string daigrams. + --> + <xsl:param name="count" select="1"/> + <xsl:param name="limit" select="1"/> + <xsl:if test="$count < $limit"> + <td style="width: 50px;" align="left"><font color="blue"><xsl:value-of select="$count"/></font></td> + <xsl:if test="$count = 1"> + <xsl:call-template name="scale"> + <xsl:with-param name="limit" select="$limit"/> + <xsl:with-param name="count" select="$count + 24"/> + </xsl:call-template> + </xsl:if> + <xsl:if test="$count > 1"> + <xsl:call-template name="scale"> + <xsl:with-param name="limit" select="$limit"/> + <xsl:with-param name="count" select="$count + 25"/> + </xsl:call-template> + </xsl:if> + </xsl:if> + </xsl:template> + + <xsl:template name="pick_color"> + <!-- + This template is used to set the color of motif markers + in the bead-on-string diagrams. + --> + <xsl:param name="index" select="1"/> + <xsl:choose> + <xsl:when test="($index mod 16) = 0">white</xsl:when> + <xsl:when test="($index mod 16) = 1">aqua</xsl:when> + <xsl:when test="($index mod 16) = 2">blue</xsl:when> + <xsl:when test="($index mod 16) = 3">red</xsl:when> + <xsl:when test="($index mod 16) = 4">fuchsia</xsl:when> + <xsl:when test="($index mod 16) = 5">yellow</xsl:when> + <xsl:when test="($index mod 16) = 6">lime</xsl:when> + <xsl:when test="($index mod 16) = 7">teal</xsl:when> + <xsl:when test="($index mod 16) = 8">#444444</xsl:when> + <xsl:when test="($index mod 16) = 9">green</xsl:when> + <xsl:when test="($index mod 16) = 10">silver</xsl:when> + <xsl:when test="($index mod 16) = 11">purple</xsl:when> + <xsl:when test="($index mod 16) = 12">olive</xsl:when> + <xsl:when test="($index mod 16) = 13">navy</xsl:when> + <xsl:when test="($index mod 16) = 14">maroon</xsl:when> + <xsl:when test="($index mod 16) = 15">black</xsl:when> + </xsl:choose> + </xsl:template> + + <xsl:template name="pick_font_color"> + <!-- + This template is used to set the font color in motif markers + in the bead-on-string diagrams. + --> + <xsl:param name="index" select="1"/> + <xsl:choose> + <xsl:when test="($index mod 16) = 0">black</xsl:when> + <xsl:when test="($index mod 16) = 1">black</xsl:when> + <xsl:when test="($index mod 16) = 2">white</xsl:when> + <xsl:when test="($index mod 16) = 3">black</xsl:when> + <xsl:when test="($index mod 16) = 4">black</xsl:when> + <xsl:when test="($index mod 16) = 5">black</xsl:when> + <xsl:when test="($index mod 16) = 6">black</xsl:when> + <xsl:when test="($index mod 16) = 7">white</xsl:when> + <xsl:when test="($index mod 16) = 8">white</xsl:when> + <xsl:when test="($index mod 16) = 9">black</xsl:when> + <xsl:when test="($index mod 16) = 10">black</xsl:when> + <xsl:when test="($index mod 16) = 11">white</xsl:when> + <xsl:when test="($index mod 16) = 12">white</xsl:when> + <xsl:when test="($index mod 16) = 13">white</xsl:when> + <xsl:when test="($index mod 16) = 14">white</xsl:when> + <xsl:when test="($index mod 16) = 15">white</xsl:when> + </xsl:choose> + </xsl:template> + + <xsl:template name="annotations"> + <!-- + This template draws the motif/sequence annotations for each + of the scanned sequence less than 10kb. + --> + <hr/> + <center> + <big><b><a name="sec_iii">SECTION III: SEQUENCE/MOTIF ANNOTATIONS</a></b></big> + </center> + <hr/> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[not (@name = preceding::cis:scanned-sequence/@name)]"> + <xsl:sort select="@name" order="ascending"/> + <xsl:variable name="sequence_length" select="@length"/> + <xsl:variable name="sequence_name" select="@name"/> + <p> + <a name="annotation_{$sequence_name}"><xsl:value-of select="$sequence_name"/></a> + <br /> + <span style="background-color: ##DDDD88;"><a href="#occurrences_{$sequence_name}">S</a></span> + <span style="background-color: #DDFFDD;"><a href="#diagram_{$sequence_name}">D</a></span> + <span style="background-color: #FFFFFF;"><a href="#button_help">?</a></span> + </p> + <p> + Length = <xsl:value-of select="$sequence_length"/> + </p> + <p> + String Length = <xsl:value-of + select="string-length(normalize-space(document('matched_sequences.xml')/matched-sequences/sequence[@name=$sequence_name]))"/> + </p> + <pre> + <table style="font-family: monospace;"> + <tbody> + <xsl:call-template name="wrap_sequence"> + <xsl:with-param name="sequence" + select="normalize-space(document('matched_sequences.xml')/matched-sequences/sequence[@name=$sequence_name])"/> + <xsl:with-param name="sequence_index" select="1"/> + <xsl:with-param name="sequence_name" select="$sequence_name"/> + </xsl:call-template> + </tbody> + </table> + </pre> + <hr/> + </xsl:for-each> + + </xsl:template> + + <xsl:template name="debugging_information"> + <!-- This template print the HTML describing the FIMO input parameters. --> + <hr/> + <center> + <big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big> + </center> + <hr/> + <p> + Command line: + </p> + <pre> + <xsl:value-of select="/fimo/command-line"/> + </pre> + <p> + Settings: + </p> + <pre> + <table> + <xsl:apply-templates select="/fimo/settings/setting[position() mod 3 = 1]"/> + </table> + </pre> + <p> + This information can be useful in the event you wish to report a + problem with the FIMO software. + </p> + <hr /> + <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span> + + </xsl:template> + + <xsl:template match="setting"> + <!-- This template prints the program settings in 2 columns --> + <tr> + <td style="padding-right: 2em"><xsl:value-of select="@name"/> = <xsl:value-of select="."/></td> + <xsl:choose> + <xsl:when test="count(following-sibling::*[name()=name(current())])"> + <td style="padding-left: 5em; padding-right: 2em"> + <xsl:value-of select="following-sibling::setting[1]/@name"/> = <xsl:value-of select="following-sibling::setting[1]"/> + </td> + <td style="padding-left: 5em; padding-right: 2em"> + <xsl:value-of select="following-sibling::setting[2]/@name"/> = <xsl:value-of select="following-sibling::setting[2]"/> + </td> + </xsl:when> + <xsl:otherwise> + <td style="padding-left: 5em; padding-right: 2em"></td> + <td align="right"></td> + </xsl:otherwise> + </xsl:choose> + </tr> + </xsl:template> + + <xsl:template name="button_help"> + <hr /> + <center> + <h3><a name="button_help">Button Help</a></h3> + </center> + <hr /> + <span style="background-color: #DDDDFF">S</span> + Links to Entrez database at <a href="http://www.ncbi.nlm.nih.gov">NCBI</a> + <span style="background-color: #DDDD88">S</span> + Links to motif occurences table(<a href="#sec_i">SECTION I</a>) + <br/> + <span style="background-color: #DDFFDD">D</span> + Links to motif occurences diagram (<a href="#sec_ii">SECTION II</a>) + <br /> + <span style="background-color: #FFDDDD">A</span> + Links to sequence/motif annotated alignments (<a href="#sec_iii">SECTION III</a>) + <br /> + <span style="background-color: #FFFFFF">?</span> + This information + <br /> + + <hr /> + <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span> + </xsl:template> + + <xsl:template name="wrap_sequence"> + <xsl:param name="sequence"/> + <xsl:param name="sequence_index"/> + <xsl:param name="sequence_name"/> + <xsl:variable name="current_sequence"> + <xsl:value-of select="substring($sequence, 1, 75)"/> + </xsl:variable> + <tr> + <td></td> + <td> + <xsl:call-template name="annotate_motif_names"> + <xsl:with-param name="sequence_index" select="$sequence_index"/> + <xsl:with-param name="sequence_name" select="$sequence_name"/> + <xsl:with-param name="current_sequence" select="$current_sequence" /> + </xsl:call-template> + </td> + </tr> + <tr> + <td style="width: 6em;"><xsl:value-of select ="$sequence_index"/></td> + <td><xsl:value-of select="$current_sequence"/></td> + </tr> + <xsl:variable name="new_sequence" select="substring($sequence, 76)"/> + <xsl:if test="string-length($new_sequence)"> + <xsl:call-template name="wrap_sequence"> + <xsl:with-param name="sequence" select="$new_sequence"/> + <xsl:with-param name="sequence_index" select="number($sequence_index) + 75"/> + <xsl:with-param name="sequence_name" select="$sequence_name"/> + </xsl:call-template> + </xsl:if> + </xsl:template> + + <xsl:template name="annotate_motif_names"> + <xsl:param name="sequence_index"/> + <xsl:param name="sequence_name"/> + <xsl:param name="input_sequence"/> + <xsl:param name="output_sequence"/> + <xsl:choose> + <xsl:when test="count(document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]) = 1"> + </xsl:when> + </xsl:choose> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]"> + <xsl:for-each select="./cis:matched-element[(@start >= $sequence_index) and (@start < ($sequence_index + 75))]"> + <xsl:sort select="@start" data-type="number" /> + <xsl:text> </xsl:text><xsl:value-of select="../../@name"/> + </xsl:for-each> + </xsl:for-each> + </xsl:template> + + <xsl:template name="annotate_pvalues"> + <xsl:param name="sequence_index"/> + <xsl:param name="sequence_name"/> + <pre> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]"> + <xsl:for-each select="./cis:matched-element[(@start >= $sequence_index) and (@start < ($sequence_index + 75))]"> + <xsl:sort select="@start" data-type="number" /> + <xsl:text> </xsl:text><xsl:value-of select="@pvalue"/> + </xsl:for-each> + </xsl:for-each> + </pre> + </xsl:template> + + <xsl:template name="annotate_best_match"> + <xsl:param name="sequence_index"/> + <xsl:param name="sequence_name"/> + <pre> + <xsl:for-each select="document('cisml.xml')/cis:cis-element-search/cis:pattern/cis:scanned-sequence[@name=$sequence_name]"> + <xsl:for-each select="./cis:matched-element[(@start >= $sequence_index) and (@start < ($sequence_index + 75))]"> + <xsl:sort select="@start" data-type="number" /> + <xsl:text> </xsl:text><xsl:value-of select="document('fimo.xml')/fimo/motif[@name=./@name]/@best-possible-match"/> + </xsl:for-each> + </xsl:for-each> + </pre> + </xsl:template> +</xsl:stylesheet> +