R. Eric Collins rec3141

## d3.phylogram.js
/*
  d3.phylogram.js
  Wrapper around a d3-based phylogram (tree where branch lengths are scaled)
  Also includes a radial dendrogram visualization (branch lengths not scaled)
  along with some helper methods for building angled-branch trees.

  d3.phylogram.build(selector, nodes, options)
    Creates a phylogram.
    Arguments:
      selector: selector of an element that will contain the SVG

## d3.phylogram.js
/*
  d3.phylogram.js
  Wrapper around a d3-based phylogram (tree where branch lengths are scaled)
  Also includes a radial dendrogram visualization (branch lengths not scaled)
  along with some helper methods for building angled-branch trees.

  d3.phylogram.build(selector, nodes, options)
    Creates a phylogram.
    Arguments:
      selector: selector of an element that will contain the SVG

## lsa_mds.R
# load required libraries
library(tm)
library(ggplot2)
library(lsa)

# 1. Prepare mock data
text <- c("transporting food by cars will cause global warming. so we should go local.",
          "we should try to convince our parents to stop using cars because it will cause global warming.",
          "some food, such as mongo, requires a warm weather to grow. so they have to be transported to canada.",
          "a typical electronic circuit can be built with a battery, a bulb, and a switch.",

## forum
Q&A

## gist:b2cc9d192d214687b575ab0cce02f5f8

while read line; do title=`echo $line | sed 's/ /+/g'`; curl -s https://api.crossref.org/works?query.title=$title&rows=1 | tr ',' '\n' | tr -d '"\' | grep ^DOI | cut -f2- -d':'; done < titles.txt > titles.bib

## gist:c6f318ae79e9695af6af14d04963f554
while read line; do curl -LH "Accept: application/x-bibtex" https://doi.org/$line    | grep -v '^\s*[<"]'; done < dois.txt > dois.bib

## gist:24090e42b4487635e8ac9f5c566ff417
while read line; do curl -s "https ://api.crossref.org/works?query=`echo $line | tr -sC '[^a-zA-Z]' '+'`" | tr "," "\n" | tr -d '"\' | grep ^DOI | cut -f2- -d':' | head -n1 | xargs -I{} curl -sLH "Accept: application/x-bibtex" https ://doi.org/{} | grep -v '^\s*[<"]'; done < file

## run-hmmer.sh
#!/bin/sh
# run hmmer using hmm files
#INDIR=$1 #directory to search for .fastq.gz files

INDIR=~/work/NPRB

cd ~/work/hmm

for hmmfile in *.hmm; do
	hmm=`basename $hmmfile .hmm`;

## srun-metaspades.sh
#!/bin/bash
NODE=bio
THREADS=7 #7 for bio, 24 for t1small
MEM=200 #128 max for t1small, 200+ for bio

mkdir -p spades-assembly
DIR='.'

#NPRB_meta_TBS.04.MEIO.R1.trimmed.fastq.gz
for PREFIX in `ls *.trimmed.fastq.gz | cut -f1-3 -d'.' | sort -u `; do

## gist:4c2cadec8e62683636d32ab52146bd7f
head -n1000 18*R1.fastq | grep -v -e '==> 18' -e '^$' | paste - - - - | cut -f2 | sort | uniq -c | sort -rn | head -n1000 | catg > 18s-top1000f.fa
	/*
	d3.phylogram.js
	Wrapper around a d3-based phylogram (tree where branch lengths are scaled)
	Also includes a radial dendrogram visualization (branch lengths not scaled)
	along with some helper methods for building angled-branch trees.

	d3.phylogram.build(selector, nodes, options)
	Creates a phylogram.
	Arguments:
	selector: selector of an element that will contain the SVG
	# load required libraries
	library(tm)
	library(ggplot2)
	library(lsa)

	# 1. Prepare mock data
	text <- c("transporting food by cars will cause global warming. so we should go local.",
	"we should try to convince our parents to stop using cars because it will cause global warming.",
	"some food, such as mongo, requires a warm weather to grow. so they have to be transported to canada.",
	"a typical electronic circuit can be built with a battery, a bulb, and a switch.",

	while read line; do title=`echo $line \| sed 's/ /+/g'`; curl -s https://api.crossref.org/works?query.title=$title&rows=1 \| tr ',' '\n' \| tr -d '"\' \| grep ^DOI \| cut -f2- -d':'; done < titles.txt > titles.bib
	#!/bin/sh
	# run hmmer using hmm files
	#INDIR=$1 #directory to search for .fastq.gz files

	INDIR=~/work/NPRB

	cd ~/work/hmm

	for hmmfile in *.hmm; do
	hmm=`basename $hmmfile .hmm`;
	#!/bin/bash
	NODE=bio
	THREADS=7 #7 for bio, 24 for t1small
	MEM=200 #128 max for t1small, 200+ for bio

	mkdir -p spades-assembly
	DIR='.'

	#NPRB_meta_TBS.04.MEIO.R1.trimmed.fastq.gz
	for PREFIX in `ls *.trimmed.fastq.gz \| cut -f1-3 -d'.' \| sort -u `; do