| # This script was created to convert a directory full | |
| # of Word Document (.docx) files into .md equivalents. It uses | |
| # pandoc to do the conversion. | |
| # | |
| # 1. Install pandoc from http://johnmacfarlane.net/pandoc/ | |
| # 2. Copy this script into the directory containing the .md files | |
| # 3. Ensure that the script has execute permissions | |
| # 4. Run the script | |
| # By default this will keep the original .md file |
| import sys | |
| from ete2 import Tree | |
| import random | |
| def get_json(node): | |
| # Read ETE tag for duplication or speciation events | |
| if not hasattr(node, 'evoltype'): | |
| dup = random.sample(['N','Y'], 1)[0] | |
| elif node.evoltype == "S": | |
| dup = "N" |
| .highlight { background: #ffffff; } | |
| .highlight .c { color: #999988; font-style: italic } /* Comment */ | |
| .highlight .err { color: #a61717; background-color: #e3d2d2 } /* Error */ | |
| .highlight .k { font-weight: bold } /* Keyword */ | |
| .highlight .o { font-weight: bold } /* Operator */ | |
| .highlight .cm { color: #999988; font-style: italic } /* Comment.Multiline */ | |
| .highlight .cp { color: #999999; font-weight: bold } /* Comment.Preproc */ | |
| .highlight .c1 { color: #999988; font-style: italic } /* Comment.Single */ | |
| .highlight .cs { color: #999999; font-weight: bold; font-style: italic } /* Comment.Special */ | |
| .highlight .gd { color: #000000; background-color: #ffdddd } /* Generic.Deleted */ |
| # This functionality has been tested and a PR has been pulled with phyloseq here: | |
| # https://github.com/joey711/phyloseq/pull/854 | |
| # | |
| # While the function has been vetted, the maintainers are very busy and the PR has not | |
| # yet been added to the main package. Below i've added some detail to explain how to parse | |
| # your silva data. It's quite easy.... | |
| source("parse_silva_taxonomy_128") |
This demo was tested on Ubuntu-16.04 which comes pre-installed with bash, Python 3.6, git, and curl. The beRi package have been built using Python 3.6. Other versions of Python have not been tested. Other operating systems have not been tested. Know bugs include renv Issue #32
WARNING: USE THIS AT YOUR OWN RISK. THIS CODE IS UNTESTED.
beRi LICENSING: beRi
renv LICENSING: renv
| [r2294@sequoia ~ $] pyenv install -v 3.7.2 | |
| /tmp/python-build.20190320123301.27082 ~ | |
| /tmp/python-build.20190320123301.27082/Python-3.7.2 /tmp/python-build.20190320123301.27082 ~ | |
| Installing Python-3.7.2... | |
| checking build system type... x86_64-pc-linux-gnu | |
| checking host system type... x86_64-pc-linux-gnu | |
| checking for python3.7... python3.7 | |
| checking for --enable-universalsdk... no | |
| checking for --with-universal-archs... no | |
| checking MACHDEP... checking for --without-gcc... no |
| Equipment_Name | RANGE | TYPE | OUTPUTNAME | WT | CRITMULT | Equipment_Name | CONTAINS | COST | PROFICIENCY | SORTKEY | CRITRANGE | DESC | SPROP | DAMAGE | SIZE | KEY | SOURCEPAGE | QUALITY | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Backpack | Goods.Container.General.Resizable | 2 | Backpack | UNLIM|Any | 2 | Backpack | Backpack | p.158 | |||||||||||
| Barrel | Goods.Container.General | 30 | Barrel | UNLIM|Any | 2 | Barrel | Barrel | p.158 | |||||||||||
| Basket | Goods.Container.General | 1 | Basket | UNLIM|Any | 0.4 | Basket | Basket | p.158 | |||||||||||
| Bedroll | Goods.General.Resizable | 5 | Bedroll | 0.1 | Bedroll | Bedroll | p.158 | ||||||||||||
| Bell | Goods.General | 0 | Bell | 1 | Bell | Bell | p.158 | ||||||||||||
| Blanket, Winter | Goods.General.Resizable | Winter Blanket | 3 | Blanket, Winter | 0.5 | Blanket, Winter | Blanket (Winter) | p.158 | |||||||||||
| Block and Tackle | Goods.General | 5 | Block and Tackle | 5 | Block and Tackle | Block and Tackle | p.158 | ||||||||||||
| Bottle | Goods.Container.General | 1 | Bottle | 1.5|Liquid=3 | 2 | Bottle | Bottle (Glass) | p.158 | |||||||||||
| Bucket | Goods.Container.General | 2 | Bucket | UNLIM|Any | 0.5 | Bucket | Bucket | p.158 |
Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.
Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.
| library(DESeq2) | |
| wrapup_for_iSEE <- function(dds, res) { | |
| # dds to vst | |
| vst <- vst(dds) | |
| # initialize the container | |
| se <- SummarizedExperiment( | |
| assays = List( | |
| counts = counts(dds), |
