smdabdoub

# Modified from https://forum.qiime2.org/t/exporting-otu-table-from-phyloseq-into-either-biom-or-text-format/19103/6
# to be directly exportable to a BIOM file using the official 'biom' command-line tool. The file-format requirements for
# a text table to be converted are listed here: 
# https://forum.qiime2.org/t/csv-to-a-qiime2-readable-format/2284/7
# This version concatenates the taxonomy ranks into a single string that is added to the OTU table as a 'taxonomy' column.
# The resulting TSV table can be converted to a BIOM-format file with the following command (outside of R):
# #biom convert -i otu_table_biom.tsv -o otu_table.biom --to-hdf5 --header-key taxonomy 
library(phyloseq)
library(readr)
library(tidyr)

smdabdoub

class Fastspar < Formula
  desc " Rapid and scalable correlation estimation for compositional data"
  homepage "https://github.com/scwatts/fastspar"
  url "https://github.com/scwatts/fastspar/archive/v0.0.5.tar.gz"
  sha256 "c4cc7682720f566da7587e555b58a688671a97235d00c33d042a7f2cd6cef20a"
  head "https://github.com/scwatts/fastspar.git"

  depends_on "armadillo" => :run
  depends_on "gsl" => :run
  depends_on "gnu-getopt" => :run

smdabdoub

# NOTE: This was done on RHEL 7.3 with JAGS v4.3.0 and rjags v4-6. It should be fairly portable, but YMMV.

# Step 1: create an MKL environment variable for use in the --with-blas option for the JAGS configure script
# the below was taken from Martyn Plummer's "Building a portable R binary with Intel tools"
# https://martynplummer.files.wordpress.com/2014/10/r-intel-fedora.pdf
# I set MKL_LIB_PATH by looking at MKL_LIBS

export MKL="-Wl,--start-group ${MKL_LIB_PATH}/libmkl_gf_lp64.a \
> ${MKL_LIB_PATH}/libmkl_gnu_thread.a \
> ${MKL_LIB_PATH}/libmkl_core.a \

smdabdoub

# Original discussion
# https://stackoverflow.com/questions/952914/making-a-flat-list-out-of-list-of-lists-in-python

# vanilla python list comprehension
flatten = lambda lst: [item for sublist in lst for item in sublist]

# with itertools
flatten_chain = lambda lst: list(itertools.chain(*lst))

# with itertools >= 2.6

smdabdoub

# based on the following:
# http://saintgimp.org/2013/01/22/merging-two-git-repositories-into-one-repository-without-losing-file-history/
# http://blog.caplin.com/2013/09/18/merging-two-git-repositories/

git clone repo_main
git clone repo_sub
cd repo_main

git remote add repo_sub ../repo_sub
git fetch repo_sub

smdabdoub

import json
import sys

def otu_name(biom_row):
    """
    Determine a simple Genus-species identifier for an OTU, if possible. 
    If OTU is not identified to the species level, name it as Unclassified (familly/genus/etc...)
    """
    tax = biom_row['metadata']['taxonomy']
    for i, lvl in enumerate(tax):

smdabdoub

➜  ~  brew install https://raw.github.com/iMichka/homebrew-science/8614633a8927be14b7e00d48a75acb66af3fc83e/insighttoolkit.rb --with-python             
######################################################################## 100.0%
==> Installing dependencies for insighttoolkit: vtk
==> Installing insighttoolkit dependency: vtk
==> Downloading http://www.vtk.org/files/release/6.0/vtk-6.0.0.tar.gz
######################################################################## 100.0%
==> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/vtk/6.0.0 -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev -DVTK_REQUIRED_OBJCXX_FLAGS='' -DVT
==> make
==> make install
==> Caveats

smdabdoub

from itertools import chain, izip

ileave = lambda *iters: list(chain(*izip(*iters)))

# full method with doctests
def interleave(*iters):
    """
    Given two or more iterables, return a list containing 
    the elements of the input list interleaved.