A report generating system for PyPPL
Project description
pyppl_report
A report generating system for PyPPL
Installation
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
Usage
Specifiation of template
pPyClone.report = """
## {{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")}})
```table
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
pPyClone.report = "file:/path/to/template.md"
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 job.report.data.yaml
under <job.outdir>
with extra data to render the report template. Beyond that, proc
attributes and args
can also be used.
For example:
job.report.data.yaml
:
description: 'A awesome report for job 1'
Then in your template, you can use it:
## {{jobs[0].description}}
Showing tables with csv/tsv file
```table
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 `csv.read`
dialect: unix
delimiter: "\t"
You may also specify width
and align
for individual columns:
width:
- .1
- .2
- .1
References
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
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