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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module delta2js</title>
</head><body bgcolor="#f0f0f8">
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
<tr bgcolor="#7799ee">
<td valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong>delta2js</strong></big></big> (version 201311261713, Nov 2013)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/home/assembly/nobackup/mummer/MUMmer3.23/hans/viewer/delta2js.py">/home/assembly/nobackup/mummer/MUMmer3.23/hans/viewer/delta2js.py</a></font></td></tr></table>
<p><tt>delta2js.py<br>
<br>
Converts mummer .delta files to javascript database for webmummer.<br>
https://github.com/sauloal/webmummer<br>
<br>
Saulo Aflitos<br>
Plant Research International - PRI<br>
Cluster Bioinformatics<br>
Wageningen University and Research Centre - WUR<br>
Centre for BioSystems Genomics - CBSG<br>
<br>
To Run:<br>
cd data<br>
rm <delta folder>/*.js<br>
delta2js.py <delta folder>/*.delta<br>
cp <delta folder>/*.js .<br>
<br>
Documentation generated by:<br>
pydoc -w delta2js<br>
<br>
License: GPL 2.0</tt></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
<tr><td bgcolor="#aa55cc"><tt> </tt></td><td> </td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="os.html">os</a><br>
</td><td width="25%" valign=top><a href="re.html">re</a><br>
</td><td width="25%" valign=top><a href="subprocess.html">subprocess</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
<tr><td bgcolor="#ee77aa"><tt> </tt></td><td> </td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="__builtin__.html#object">__builtin__.object</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="delta2js.html#exp">exp</a>
</font></dt></dl>
</dd>
</dl>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="exp">class <strong>exp</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>Exporter Class: exports database headers (title, axis labels and limits) and, uppon<br>
receiving each coordinates, append it to the array.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="exp-__init__"><strong>__init__</strong></a>(self, outfile, refName, refChrom, tgtName, tgtChrom, status, title<font color="#909090">='title'</font>, xlabel<font color="#909090">='xlabel'</font>, ylabel<font color="#909090">='ylabel'</font>)</dt><dd><tt>Accepts output file, title and axis labels.<br>
Initialize limits.</tt></dd></dl>
<dl><dt><a name="exp-add"><strong>add</strong></a>(self, sense, reg)</dt><dd><tt>Filters from register only the necessary information.<br>
Calls self.<strong>append</strong>;</tt></dd></dl>
<dl><dt><a name="exp-append"><strong>append</strong></a>(self, x1, y1, x2, y2, name, sense, q)</dt><dd><tt>Adds query name to database of names (a list of all names).<br>
Exports only species ID (index of the scaffold name in the database of names);<br>
<br>
Replaces sense for 0/1;<br>
<br>
Updates min and max positions;</tt></dd></dl>
<dl><dt><a name="exp-close"><strong>close</strong></a>(self)</dt><dd><tt>Exports min/max;<br>
Exports query species list;<br>
Closes filehandle;</tt></dd></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#eeaa77">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
<td width="100%"><dl><dt><a name="-genCoords"><strong>genCoords</strong></a>(exporter, scafOrder, scafLens)</dt><dd><tt>Check sanity of data and adds data to exporter.<br>
Converts query coordnates to Y coordinates where scaffolds are ordered and their lengths sum<br>
to create a single Y axis.</tt></dd></dl>
<dl><dt><a name="-main"><strong>main</strong></a>()</dt><dd><tt>Parse all input files names, exports them to databases and creates index of all files.</tt></dd></dl>
<dl><dt><a name="-parseDelta"><strong>parseDelta</strong></a>(delta)</dt><dd><tt>Converts .delta to .coords (if needed) and parses .coords file.</tt></dd></dl>
<dl><dt><a name="-parseFN"><strong>parseFN</strong></a>(infile)</dt><dd><tt>Parses file name to extract species information</tt></dd></dl>
</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
<tr><td bgcolor="#55aa55"><tt> </tt></td><td> </td>
<td width="100%"><strong>__author__</strong> = 'Saulo Aflitos'<br>
<strong>__credits__</strong> = 'mummer, WUR, PRI, CBSG'<br>
<strong>__date__</strong> = 'Nov 2013'<br>
<strong>__version__</strong> = '201311261713'<br>
<strong>compulsory</strong> = None<br>
<strong>dry_run</strong> = None<br>
<strong>forbidden</strong> = None<br>
<strong>labelFields</strong> = None<br>
<strong>pointFmt</strong> = '%d,%d,%d,%d,%d,%d,%.2f,'<br>
<strong>statusMatch</strong> = None<br>
<strong>titleFmt</strong> = None<br>
<strong>xlabelFmt</strong> = None<br>
<strong>ylabelFmt</strong> = None</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
<tr><td bgcolor="#7799ee"><tt> </tt></td><td> </td>
<td width="100%">Saulo Aflitos</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Credits</strong></big></font></td></tr>
<tr><td bgcolor="#7799ee"><tt> </tt></td><td> </td>
<td width="100%">mummer, WUR, PRI, CBSG</td></tr></table>
</body></html>