Output overall stats and log files

biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.

http://biomedicalinformaticsgroup.github.io/Sargasso/

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Output overall stats and log files #39

Closed lweasel closed 8 years ago

lweasel commented 8 years ago

Prompted by this blog post:

http://www.tallphil.co.uk/writing-good-log-files/

I think we could output the following at the top level of the output directory:

a log file (TSV or JSON format?) recording the tool version, run date and time, and options that the tool was run with
an overall stats file (again, TSV or JSON format) with the numbers of accepted, rejected and ambiguous reads for each species. I think that we're currently doing this per-block, but it would be really nice to sum them up so that the user doesn't have to do that themselves.

s-heron commented 8 years ago

I concur. Unless you're a particular fan of JSON (I've never really used it), perhaps TSV to keep it simple and readable.

lweasel commented 8 years ago

I think TSV is fine, good balance between machine and human readable, and can be opened straight into Excel or suchlike.

s-heron commented 8 years ago

I added an overall stats file in in my most recent commit

s-heron commented 8 years ago

I've added code to the species-separator.py file to write an execution log with a time/date stamp and parameter listing

lweasel commented 8 years ago

I've tweaked the overall stats file to sum up the block file numbers into counts per-sample. This was what I originally intended, but I entirely failed to articulate it!