Mercurial > repos > holtgrewe > ngs_roi
diff roi_table.py @ 0:61d9bdb6d519 draft
Uploaded
| author | holtgrewe |
|---|---|
| date | Thu, 18 Apr 2013 08:03:38 -0400 |
| parents | |
| children | 0ac4f6f3d984 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/roi_table.py Thu Apr 18 08:03:38 2013 -0400 @@ -0,0 +1,176 @@ +#!/usr/bin/env python +"""ROI Table Generator + +Generates a HTML page with a table of ROI record details. Besides showing the +numeric ROI information, it also gives little roi plots in a column. + +For the little ROI plots, it calls the program roi_plot_thumbnails that has to +be in the PATH. +""" + +__author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>' +__copyright__ = 'Copyring 2013, Freie Universitaet Berlin' +__license__ = 'BSD 3-clause' + + +# TODO(holtgrew): Actually call roi_plot_thumbnails +# TODO(holtgrew): from __future__ use print_function + + +import argparse +import math +import os.path +import sys + +import Cheetah.Template + +import ngs_roi.app +import ngs_roi.argparse +import ngs_roi.io + + +# Main template. +PAGE_TPL = """ +<html> + <head><title>ROI Table</title></head> + <body> + <h1>ROI Table</h1> + $table + </body> +</html> +""" + +# Template for a table. +TABLE_TPL = """ +<table border="1"> + <tr> + <th>plot</th> + <th>chr</th> + <th>start</th> + <th>end</th> + <th>name</th> + <th>length</th> + <th>strand</th> + <th>max_count</th> + #for i, key in enumerate($data_keys) + <th>$key</th> + #end for + </tr> + #for id, roi in enumerate($records) + <tr> + <td><div style="width:${args.plot_width}; margin:2px; height:${args.plot_height+1}; background:url(thumbnail_${imgId($id)}.png) -${imgX($id)} -${imgY($id)};"></div></td> + <td>$roi.ref</td> + <td style="text-align:right;">$fmtPos($roi.start_pos + 1)</td> + <td style="text-align:right;">$fmtPos($roi.end_pos)</td> + <td><a href="$href($roi)">$roi.region_name</a></td> + <td style="text-align:right;">$fmtPos($roi.region_length)</td> + <td style="text-align:center;">$roi.strand</td> + <td style="text-align:right;">$roi.max_count</td> + #for i, key in enumerate($data_keys) + <td>$roi.data[$i]</td> + #end for + </tr> + #end for +</table> +""" + + +class RoiTable(object): + """A table of ROI records with small plots.""" + + def __init__(self, args, keys, records, app): + self.args = args + self.keys = keys + self.records = records + self.app = app + + def tplFuncs(self): + def intWithCommas(x): + if type(x) not in [type(0), type(0L)]: + raise TypeError("Parameter must be an integer.") + if x < 0: + return '-' + intWithCommas(-x) + result = '' + while x >= 1000: + x, r = divmod(x, 1000) + result = ",%03d%s" % (r, result) + return "%d%s" % (x, result) + + def imgId(idx): + """Image id from roi record id.""" + return idx / (self.args.num_rows * self.args.num_cols) + + def imgX(idx): + """x position in image from record id.""" + x = idx % self.args.num_cols + res = x * self.args.plot_width + if x > 0: + res += (x - 1) * 2 + return res + + def imgY(idx): + """y position in image from record id.""" + y = idx / self.args.num_cols + res = y * self.args.plot_height + res += y * 2 + return res + + return {'fmtPos': intWithCommas, 'imgId': imgId, 'imgX': imgX, 'imgY': imgY} + + def render(self): + """Returns string with rendered table.""" + vals = {'data_keys': self.keys, 'records': self.records, 'args': self.args, + 'href': lambda x:self.app.buildHref(x.ref, x.start_pos, x.end_pos)} + vals.update(self.tplFuncs()) + t = Cheetah.Template.Template(TABLE_TPL, searchList=vals) + return str(t) + + +class TableApp(ngs_roi.app.App): + def __init__(self, args): + # Call parent's constructor and create output directory. + ngs_roi.app.App.__init__(self, args) + self.prepareOutDir() + + def run(self): + # Load ROI records. + print >>sys.stderr, 'Loading ROI' + records = ngs_roi.io.load(self.args.in_file, self.args.max_rois) + keys = [] + if records: + keys = records[0].data_keys + + # Create plots. + print >>sys.stderr, 'Creating plots...' + runner = ngs_roi.app.PlotThumbnailsRunner(self.args) + runner.run() + + # Create table. + print >>sys.stderr, 'Creating table...' + self.createHtml(self.args.out_file, keys, records) + return 0 + + def createHtml(self, file_name, keys, records): + print >>sys.stderr, 'Writing %s' % self.args.out_file + vals = {'table': RoiTable(self.args, keys, records, self).render()} + t = Cheetah.Template.Template(PAGE_TPL, searchList=vals) + with open(self.args.out_file, 'wb') as f: + f.write(str(t)) + + +def main(): + parser = argparse.ArgumentParser(description='Plot ROI file.') + + ngs_roi.argparse.addFileArguments(parser) + ngs_roi.argparse.addPlotGridArguments(parser, default_plot_height=60, + default_plot_width=90) + ngs_roi.argparse.addLinkArguments(parser) + args = parser.parse_args() + ngs_roi.argparse.applyFileDefaults(args) + + app = TableApp(args) + return app.run() + + +if __name__ == '__main__': + sys.exit(main())