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Preprocessing notebook #126
Preprocessing notebook #126
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Removes files not up for review in this pull request
Removes data generated by the preprocessing notebook
Bumping this, since the tables are being distributed. @wasade, @ElDeveloper , @cuttlefishh: The |
few comments below: beta diversity likely includes archaea as well boolian -> boolean I don't think pandas was described as a requirement for the notebook beta diversity hyperlink in "beta diversity parameters" doesn't work ag is picked against Greengenes 13_8 greengenes -> Greengenes in split directories and files, why are the underscores escaped? eg split_raw_dir. this happens in multiple places when describing variables, like file pattern fill-in, etc why does the notebook download the preprocessed data if the point is to produce the preprocessed data? the hyperlinks for the references don't work, look like they're formatted incorrectly |
I only listed the requirements that were not superseded by QIIME or are I think the issue is mixing markdown and HTML. It worked in my Safari and The escapes are there because it explicitly forces the underscores to be I can't set up an explicit way to download the FTP as a hyperlink in an On Mon, Mar 30, 2015 at 8:17 AM, Daniel McDonald notifications@github.com
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Hyperlinks work with ftp, just use: ftp://ftp.microbio.me/foo/bar. Pandas is not a dep of any of those IIRC, but might be wrong
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When I tried to make them in IPython, the hyperlink hover-over is a curser, not the little link-click hand. I looked over what I could find in StackOverflow, python and IPython documentation, but I couldn't find a satisfactory solution for linking to an ftp in the markdown cells. Pandas is a scikit-bio dependency AFAIK. |
Ah yeah, this is a known problem with Markdown. On (Mar-30-15|10:58), J W Debelius wrote:
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With that in mind, how would you prefer to handle this? The solutions I can come up with include something like the current I think all three have advantages and drawbacks. On Mon, Mar 30, 2015 at 11:00 AM, Yoshiki Vázquez Baeza <
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This fixes the markdown issues with appearance and the links. The download flag is still included in the notebook. I'd like to get this merged sooner because it reflects tables we're sending out with the manuscript. It can live in my repo indefinitely, but it would be better to have it in master. |
That notebook is 🌟 amazing 🌟! |
@ElDeveloper, merge? |
@ElDeveloper: Any update on review? Thank you for your help! |
@jwdebelius and I are going through the notebook, we hope to have a final version around 4:00 pm PDT today. |
Running a little behind. Thank you for all the awesome help today, @ElDeveloper. I had one question: you suggested applying the |
My main suggestion for using the euclidian distance function in scipy, On (Apr-13-15|20:20), J W Debelius wrote:
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Fixes syntax and functions calls
Thanks @jwdebelius |
A notebook for the generation of clean, consistent tables for use in downstream analyses. Rather than spending half a notebook trying to get data in a desired format, this centralizes the process.
Notebook can be viewed here.
This relies on files in #125.