Source code for sequana.modules_report.trf
# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
# Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>,
# <d.desvillechabrol@gmail.com>
# Rachel Legendre <rachel.legendre@pasteur.fr>
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.readthedocs.io
#
##############################################################################
"""Report dedicated to BAM file
.. autosummary::
TRFModule
"""
import os
from sequana import TRF
from sequana.lazy import pandas as pd
from sequana.lazy import pylab
from sequana.modules_report.base_module import SequanaBaseModule
from sequana.utils.datatables_js import DataTable
from sequana.utils.df2html import df2html
__all__ = ["TRFModule"]
[docs]
class TRFModule(SequanaBaseModule):
"""Report dedicated to TRF file"""
def __init__(self, trf_input, output_filename=None):
super().__init__()
self.trf = TRF(trf_input)
self.title = "TRF Report"
self.create_report_content()
self.create_html(output_filename)
[docs]
def create_report_content(self):
self.sections = list()
self.add_info()
self.add_table()
self.add_images_section()
[docs]
def add_info(self):
html = "<br>".join(self.trf.__repr__().split("\n"))
self.sections.append({"name": "Information", "anchor": "info", "content": html})
[docs]
def add_table(self):
datatable = DataTable(self.trf.df, "result", index=True)
datatable.datatable.datatable_options = {
"scrollX": "300px",
"pageLength": 15,
"scrollCollapse": "true",
"dom": "tBifp",
"paging": "true",
"buttons": ["copy", "csv"],
}
js = datatable.create_javascript_function()
html_tab = datatable.create_datatable(float_format="%.3g")
html = ""
html += "{} {}".format(html_tab, js)
self.sections.append({"name": "TRF results", "anchor": "results", "content": html})
[docs]
def add_images_section(self):
style = "width:65%"
import pylab
pylab.ioff()
def plotter1(filename):
pylab.clf()
self.trf.hist_entropy()
pylab.savefig(filename)
html1 = self.create_embedded_png(plotter1, "filename", style=style)
def plotter2(filename):
pylab.clf()
self.trf.hist_period_size()
pylab.savefig(filename)
html2 = self.create_embedded_png(plotter2, "filename", style=style)
self.sections.append({"name": "Image", "anchor": "table", "content": html1 + html2})
