Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

A report generating system for PyPPL

Project description


Pypi Github PyPPL PythonVers docs Travis building Codacy Codacy coverage

A report generating system for PyPPL


Requires pandoc 2.7+ (and wkhtmltopdf 0.12.4+ when creating PDF reports)

pyppl_report requires pandoc/wkhtmltopdf to be installed in $PATH

pip install pyppl_report


Specifiation of template = """
## {{title}}

PyClone[1] is a tool using Probabilistic model for inferring clonal population structure from deep NGS sequencing.

![Similarity matrix]({{path.join(job.o.outdir, "plots/loci/similarity_matrix.svg")}})

caption: Clusters
file: "{{path.join(job.o.outdir, "tables/cluster.tsv")}}"
rows: 10

[1]: Roth, Andrew, et al. "PyClone: statistical inference of clonal population structure in cancer." Nature methods 11.4 (2014): 396.

# or use a template file = "file:/path/to/"

Generating report

PyPPL().start(pPyClone).run().report('/path/to/report', title = 'Clonality analysis using PyClone')


Extra data for rendering

You can generate a YAML file named under <job.outdir> with extra data to render the report template. Beyond that, proc attributes and args can also be used.

For example:

description: 'A awesome report for job 1'

Then in your template, you can use it:

## {{jobs[0].description}}

Showing tables with csv/tsv file

caption    : An awesome table
file       : /path/to/csv/tsv/file
header     : true
width      : 1   # width of each column
total_width: .8  # total width of the table
align      : default # alignment of each column
rows       : 10  # max rows to show
cols       : 0   # max cols to show, default: 0 (show all)
csvargs    : # csvargs for ``
	dialect: unix
	delimiter: "\t"

You may also specify width and align for individual columns:

  - .1
  - .2
  - .1


We use [1], [2] ... to link to the references, so HTML links have to be in-place (in the format of [text](link) instead of [text][link-index]). All references from different processes will be re-ordered and combined.

Advanced usage


Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pyppl-report, version 0.4.0
Filename, size File type Python version Upload date Hashes
Filename, size pyppl_report-0.4.0-py3-none-any.whl (173.7 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size pyppl_report-0.4.0.tar.gz (169.4 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page