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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:47:53 -0500 |
| parents | 9071e359b9a3 |
| children |
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<?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>