Module epijinn.reports

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# Copyright 2024 Edinburgh Genome Foundry, University of Edinburgh

#

# This file is part of EpiJinn.

#

# EpiJinn is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

#

# EpiJinn is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

#

# You should have received a copy of the GNU General Public License along with Ediacara. If not, see <https://www.gnu.org/licenses/>.

from datetime import datetime

import os

from pdf_reports import (

    add_css_class,

    dataframe_to_html,

    pug_to_html,

    style_table_rows,

    write_report,

)

import pdf_reports.tools as pdf_tools

from .version import __version__

THIS_PATH = os.path.dirname(os.path.realpath(__file__))

ASSETS_PATH = os.path.join(THIS_PATH, "report_assets")

BEDMETHYLITEMGROUP_REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "report.pug")

STYLESHEET = os.path.join(ASSETS_PATH, "report_style.css")

def epijinn_pug_to_html(template, **context):

    now = datetime.now().strftime("%Y-%m-%d")

    defaults = {

        "sidebar_text": "Generated on %s by EpiJinn (version %s)" % (now, __version__),

        "epijinn_logo_url": os.path.join(ASSETS_PATH, "imgs", "epijinn.png"),

    }

    for k in defaults:

        if k not in context:

            context[k] = defaults[k]

    return pug_to_html(template, **context)

def tr_modifier_for_bed_table(tr):

    tds = list(tr.find_all("td"))

    if len(tds) == 0:

        return

    methylated = tds[-1]  # last column shows status

    if methylated.text == "1":

        add_css_class(tr, "negative")

    # else:

    #     add_css_class(tr, "positive")

def write_bedmethylitemgroup_report(

    bedmethylitemgroup, pdf_file="report.pdf", html_file=None

):

    """Write a methylation analysis report with a PDF summary.

    **Parameters**

    **bedmethylitemgroup**

    > `BedmethylItemGroup` instance.

    **pdf_file**

    > Optional PDF file name (`str`). Specify `None` to omit.

    **html_file**

    > Optional HTML file name (`str`). The PDF is created from this HTML data.

    """

    for bedmethylitem in bedmethylitemgroup.bedmethylitems:

        bedmethylitem.bedmethylitem_figure_data = pdf_tools.figure_data(

            bedmethylitem.fig, fmt="svg"

        )

        for bedresult in bedmethylitem.results:

            bedresult.bed_pdf = dataframe_to_html(

                bedresult.bed,

                extra_classes=(

                    "ui",

                    "compact",

                    "celled",

                    # "striped",

                    "table",

                    "groups",

                ),

                use_default_classes=False,

            )

            bedresult.bed_pdf = style_table_rows(

                bedresult.bed_pdf, tr_modifier_for_bed_table

            )

            if bedresult.img_created:

                bedresult.figure_data = pdf_tools.figure_data(bedresult.plot, fmt="svg")

    html = epijinn_pug_to_html(

        BEDMETHYLITEMGROUP_REPORT_TEMPLATE, bedmethylitemgroup=bedmethylitemgroup

    )

    if html_file:

        with open(html_file, "w") as html_output:

            html_output.write(html)

    if pdf_file:

        write_report(html, pdf_file, extra_stylesheets=(STYLESHEET,))

Variables

ASSETS_PATH

BEDMETHYLITEMGROUP_REPORT_TEMPLATE

STYLESHEET

THIS_PATH

Functions

epijinn_pug_to_html

def epijinn_pug_to_html(
    template,
    **context
)

View Source

def epijinn_pug_to_html(template, **context):

    now = datetime.now().strftime("%Y-%m-%d")

    defaults = {

        "sidebar_text": "Generated on %s by EpiJinn (version %s)" % (now, __version__),

        "epijinn_logo_url": os.path.join(ASSETS_PATH, "imgs", "epijinn.png"),

    }

    for k in defaults:

        if k not in context:

            context[k] = defaults[k]

    return pug_to_html(template, **context)

tr_modifier_for_bed_table

def tr_modifier_for_bed_table(
    tr
)

View Source

def tr_modifier_for_bed_table(tr):

    tds = list(tr.find_all("td"))

    if len(tds) == 0:

        return

    methylated = tds[-1]  # last column shows status

    if methylated.text == "1":

        add_css_class(tr, "negative")

    # else:

    #     add_css_class(tr, "positive")

write_bedmethylitemgroup_report

def write_bedmethylitemgroup_report(
    bedmethylitemgroup,
    pdf_file='report.pdf',
    html_file=None
)

Write a methylation analysis report with a PDF summary.

Parameters

bedmethylitemgroup

BedmethylItemGroup instance.

pdf_file

Optional PDF file name (str). Specify None to omit.

html_file

Optional HTML file name (str). The PDF is created from this HTML data.

View Source

def write_bedmethylitemgroup_report(

    bedmethylitemgroup, pdf_file="report.pdf", html_file=None

):

    """Write a methylation analysis report with a PDF summary.

    **Parameters**

    **bedmethylitemgroup**

    > `BedmethylItemGroup` instance.

    **pdf_file**

    > Optional PDF file name (`str`). Specify `None` to omit.

    **html_file**

    > Optional HTML file name (`str`). The PDF is created from this HTML data.

    """

    for bedmethylitem in bedmethylitemgroup.bedmethylitems:

        bedmethylitem.bedmethylitem_figure_data = pdf_tools.figure_data(

            bedmethylitem.fig, fmt="svg"

        )

        for bedresult in bedmethylitem.results:

            bedresult.bed_pdf = dataframe_to_html(

                bedresult.bed,

                extra_classes=(

                    "ui",

                    "compact",

                    "celled",

                    # "striped",

                    "table",

                    "groups",

                ),

                use_default_classes=False,

            )

            bedresult.bed_pdf = style_table_rows(

                bedresult.bed_pdf, tr_modifier_for_bed_table

            )

            if bedresult.img_created:

                bedresult.figure_data = pdf_tools.figure_data(bedresult.plot, fmt="svg")

    html = epijinn_pug_to_html(

        BEDMETHYLITEMGROUP_REPORT_TEMPLATE, bedmethylitemgroup=bedmethylitemgroup

    )

    if html_file:

        with open(html_file, "w") as html_output:

            html_output.write(html)

    if pdf_file:

        write_report(html, pdf_file, extra_stylesheets=(STYLESHEET,))