Reports documentation¶

Current version: 0.3.1, February 16, 2017

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Python version:	Python 2.7, 3.4 and 3.5
documentation:	On readthedocs
Issues:	Please fill form on On github

Reports is a simple Python package that provides tools to create HTML documents. It is based on a set of JINJA templates and a class called Report. In addition tools such as HTMLTable can help in the creation of HTML table to be included in the report.

The package relies on Pandas for the HTML table creation, as shown in the example below.

We provide a simple JINJA example (stored with the pacakge in ./share/data/templates/generic directory) and we let the users design their own templates.

This is used in GDSCTools and Sequana packages.

Usage¶

Example¶

Here below, we show the code used to create this example.

# We will create a Report and insert an HTML table in it
from reports import Report, HTMLTable

# Let us create some data. It will be a HTML table built using Pandas
# but you could create the HTML table code yourself.
import pandas as pd

# create a dataframe to play with. Note that there is a numeric column
# In addition, there is a column (Entry name) that will be transformed into URLs
df = pd.DataFrame({
    "Entry name":["ZAP70_HUMAN", "TBK1_HUMAN"],
    "Entry": ["P43403", "Q9UHD2"],
    "Frequency": [0.5,0.9]})

# From reports, we convert the dataframe into a HTMLTable
table = HTMLTable(df)

# a numeric column can be colorized
table.add_bgcolor('Frequency', cmap="copper")

# part of URLs can be added to the content of a column
table.add_href('Entry', url='http://uniprot.org/uniprot/', suffix="")
html = table.to_html()

# Create a generic report. It has a set of tags that can be filled
# using the **jinja** attribute.
r = Report("generic")

# set the **summary** tag with the HTML code of the table
r.jinja['summary'] = html

# Generate and show the report
r.create_report(onweb=True)

See the results in example

Using your own JINJA template¶

Create a directory called test and add a file called index.html

Add this code:

<h1> {{ title }} </h1>
<p> Number of reads : {{ reads }} </p>

Now, create your HTML files:

from reports import Report
report = Report("test")
report.jinja['title'] = 'Simple Example'
report.jinja['reads'] = "123456"
report.create_report(onweb=True)