# 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>
#
# 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
#
##############################################################################
"""Module to write coverage report"""
import glob
import io
import os
import colorlog
from sequana.lazy import pandas as pd
from sequana.lazy import pylab
from sequana.modules_report.base_module import SequanaBaseModule
from sequana.utils import config
logger = colorlog.getLogger(__name__)
from sequana.utils.datatables_js import DataTable
[docs]
class FastQStatsModule(SequanaBaseModule):
"""Write HTML report of fastq stats analysis."""
def __init__(self, input_directory, path_to_fastqc, output_filename=None, tag_R1="_R1_"):
"""
:param input_directory: where to find the json and boxplot image. The
path where to find the data does not matter since the JSON and PNG
will be embedded.
:param path_to_fastqc: This must be provided by the user. This is the
directory where will be found the original FastQC reports. This can
be infered but is prone to error so for now, we must provide this
argument.
:param output_filename: if not provided, the HTML is not created.
::
from sequana.modules_report.fastq_stats import FastQStatsModule
ff = FastQStatsModule("./SAMPLE/fastq_stats_samples", "fastqc_samples",
"test.html")
"""
super().__init__()
self.path_to_fastqc = path_to_fastqc
self.directory = input_directory
self.create_report_content()
if output_filename:
self.create_html(output_filename)
[docs]
def create_report_content(self):
"""Generate the sections list to fill the HTML report."""
self.sections = list()
self.add_stats()
def _get_files(self, pattern):
# !! need to sort the files so that R1 appears before R2
filenames = sorted(glob.glob(self.directory + os.sep + pattern))
if len(filenames) == 2:
mode = "pe"
elif len(filenames) == 1:
mode = "se"
elif len(filenames) == 0:
return
else:
logger.warning("FastQStatsModule: more than 2 files " "matched the pattern %s" % pattern)
return
return filenames, mode
[docs]
def get_stats(self):
import pandas as pd
filenames, mode = self._get_files("*.json")
if mode == "pe":
df1 = pd.read_json(filenames[0])
df2 = pd.read_json(filenames[1])
df = pd.concat([df1, df2])
# Should have been sorted !
df.index = ["R1", "R2"]
else:
df = pd.read_json(filenames[0])
df.index = ["R1"]
df = df[
[
"A",
"C",
"G",
"T",
"N",
"n_reads",
"mean quality",
"GC content",
"average read length",
"total bases",
]
]
for this in "ACGTN":
df[this] /= df["total bases"]
df[this] *= 100
return df
def _get_stats_section(self, tablename="stats"):
self.df_stats = self.get_stats()
filenames, mode = self._get_files("*boxplot.png")
datatable = DataTable(self.df_stats, tablename, index=True)
datatable.datatable.datatable_options = {
"scrollX": "300px",
"pageLength": 15,
"scrollCollapse": "true",
"dom": "rtpB",
"paging": "false",
"buttons": ["copy", "csv"],
}
js = datatable.create_javascript_function()
html_tab = datatable.create_datatable(float_format="%.3g")
html = """<p>The following table gives some basic statistics about the data before any filtering.
The A, C, G, T, N columns report the percentage of each bases in the overall sequences.
The GC content is provided in percentage as well. </p>
<div>{} {}</div>
<div>""".format(
html_tab, js
)
html += """
<p>The following figure(s) gives the average quality (red line) of raw reads
(500,000 at max). The x-axis being the length of the reads. The yellow
enveloppe gives the variation of the quality (1 standard deviation).</p>
<p> Click on the image to jump to a full FastQC report.</p>"""
if len(filenames) == 2:
width = "49"
else:
width = "65"
filename = os.path.split(filenames[0])[1].replace("_boxplot.png", "_fastqc.html")
href = self.path_to_fastqc + os.sep + filename
html += """
<figure style="float:left; width:{}%; padding:0px; margin:0px;">
<a href="{}">{}</a>
<figcaption style="font-style:italic">Fig1: R1 reads</figcaption>
</figure>""".format(
width, href, self.png_to_embedded_png(filenames[0])
)
if len(filenames) == 2:
filename = os.path.split(filenames[1])[1].replace("_boxplot.png", "_fastqc.html")
href = self.path_to_fastqc + os.sep + filename
html += """
<figure style="float:right; width:{}%; padding:0px; margin:0px;">
<a href="{}">{}</a>
<figcaption style="font-style:italic">Fig2: R2 reads</figcaption>
</figure>""".format(
width, href, self.png_to_embedded_png(filenames[1])
)
return html
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def add_stats(self):
html = self._get_stats_section()
self.sections.append({"name": "Stats inputs", "anchor": "stats", "content": html})
