Module seqreport.reports

View Source

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")

SEQCOLLECTION_REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "seq_report.pug")

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

def end_pug_to_html(template, **context):

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

    defaults = {

        "sidebar_text": "Generated on %s by Seq Report (version %s)"

        % (now, __version__),

    }

    for k in defaults:

        if k not in context:

            context[k] = defaults[k]

    return pug_to_html(template, **context)

def write_pdf_report(target, seqcollection):

    """Write a sequence collection report with a PDF summary.

    **Parameters**

    **target**

    > Path for PDF file.

    **seqcollection**

    > `SeqCollection` instance.

    """

    html = end_pug_to_html(SEQCOLLECTION_REPORT_TEMPLATE, seqcollection=seqcollection)

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

Variables

ASSETS_PATH

SEQCOLLECTION_REPORT_TEMPLATE

STYLESHEET

THIS_PATH

Functions

end_pug_to_html

def end_pug_to_html(
    template,
    **context
)

View Source

def end_pug_to_html(template, **context):

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

    defaults = {

        "sidebar_text": "Generated on %s by Seq Report (version %s)"

        % (now, __version__),

    }

    for k in defaults:

        if k not in context:

            context[k] = defaults[k]

    return pug_to_html(template, **context)

write_pdf_report

def write_pdf_report(
    target,
    seqcollection
)

Write a sequence collection report with a PDF summary.

Parameters

target

Path for PDF file.

seqcollection

SeqCollection instance.

View Source

def write_pdf_report(target, seqcollection):

    """Write a sequence collection report with a PDF summary.

    **Parameters**

    **target**

    > Path for PDF file.

    **seqcollection**

    > `SeqCollection` instance.

    """

    html = end_pug_to_html(SEQCOLLECTION_REPORT_TEMPLATE, seqcollection=seqcollection)

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