Python库 | pyppl-report-0.0.1.tar.gz

# pyppl-report A report generating system for [PyPPL][1] ## Installation ```shell pip install pyppl-report ``` ## Usage ### Specifiation of template ````python pPyClone.report = """ ## {{proc.desc}} PyClone[1] is a tool using Probabilistic model for inferring clonal population structure from deep NGS sequencing. }}) ```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 ```python 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`: ```yaml title: 'A awesome report for job 1' ``` Then in your template, you can use it: ```markdown ## {{jobs[0].title}} ``` ### Showing tables with csv/tsv file ````markdown ```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: ```yaml 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. [1]: https://github.com/pwwang/PyPPL