Josh Herr jrherr

## excel_my_barplot.R
x <- data.frame(d=runif(12), g=rep(1:4, each =3))

my.col <- c("deepskyblue3","darkorange2","darkgray","gold")

spacer <- c(1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1)

bw <- 0.8

xmax <- (sum(spacer) * bw) + (nrow(x) * bw)

## read_hdf5_biom.R
source("http://bioconductor.org/biocLite.R")
biocLite(c("rhdf5","biom"))
library(rhdf5)
library(biom)

# This generates the matrix columns-wise
generate_matrix <- function(x){
	indptr  = x$sample$matrix$indptr+1
	indices = x$sample$matrix$indices+1
	data    = x$sample$matrix$data

## fq-strip-contam.sh
# -q: output in Fastq format
# -Q: ignore BAM quality flags
# -P: paired-end data
bam2fastx -qQP -o clean.fq <(bwa mem contaminants.fasta reads.1.fq reads.2.fq | \
                             perl -ne '@v = split(/\t/); print if(m/^@/ or ($v[1] & 4 and $v[1] & 8))' | \
                             samtools view -bhS -)

## genome_plots.r
source("http://bioconductor.org/biocLite.R")
biocLite("genomes")

library(genomes)
library(ggplot2)

valid <- c("released", "created", "submitted")

data(proks)
update(proks)

## search_download.md

      
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                jrherr
                / search_download.md
            
            
              Last active
              August 29, 2015 14:26
                — forked from sckott/search_download.md
            
              
                occ_search and occ_download 
              
          
    to get similar results for GBIF search and download APIs

Load rgbif
library("rgbif")
occ_search() method


## 01.cmake
Wed Jun 10 19:52:40 +0000 2015

cmake
..
-DCMAKE_C_FLAGS_RELEASE=
-DCMAKE_CXX_FLAGS_RELEASE=
-DCMAKE_INSTALL_PREFIX=/home/ubuntu/.linuxbrew/Cellar/spades/3.5.0
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_FIND_FRAMEWORK=LAST
-DCMAKE_VERBOSE_MAKEFILE=ON

## remove_redundant_sequences
sed -e '/^>/s/$/@/' -e 's/^>/#/' name.fasta | tr -d '\n' | tr "#" "\n" | tr "@" "\t" | sort -u -t '  ' -f -k 2,2  | sed -e 's/^/>/' -e 's/\t/\n/'

## gist:1ae494fc5396a8b49cd4
# kill all qsub jobs
qselect -u $USER -S -Q | xargs qdel

## bamfilter_oneliners.md

      
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                jrherr
                / bamfilter_oneliners.md
            
            
              Last active
              September 9, 2015 15:19
                — forked from davfre/bamfilter_oneliners.md
            
          
    SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)

@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please comment or extend with additional/faster/better solutions.
BWA mapping (using piping for minimal disk I/O)

  
## gist:2c5fed226a1a63f5643a
sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.name}\1 \2/g" $input > $output
	x <- data.frame(d=runif(12), g=rep(1:4, each =3))

	my.col <- c("deepskyblue3","darkorange2","darkgray","gold")

	spacer <- c(1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1)

	bw <- 0.8

	xmax <- (sum(spacer) * bw) + (nrow(x) * bw)
	source("http://bioconductor.org/biocLite.R")
	biocLite(c("rhdf5","biom"))
	library(rhdf5)
	library(biom)

	# This generates the matrix columns-wise
	generate_matrix <- function(x){
	indptr = x$sample$matrix$indptr+1
	indices = x$sample$matrix$indices+1
	data = x$sample$matrix$data
	# -q: output in Fastq format
	# -Q: ignore BAM quality flags
	# -P: paired-end data
	bam2fastx -qQP -o clean.fq <(bwa mem contaminants.fasta reads.1.fq reads.2.fq \| \
	perl -ne '@v = split(/\t/); print if(m/^@/ or ($v[1] & 4 and $v[1] & 8))' \| \
	samtools view -bhS -)
	source("http://bioconductor.org/biocLite.R")
	biocLite("genomes")

	library(genomes)
	library(ggplot2)

	valid <- c("released", "created", "submitted")

	data(proks)
	update(proks)
	Wed Jun 10 19:52:40 +0000 2015

	cmake
	..
	-DCMAKE_C_FLAGS_RELEASE=
	-DCMAKE_CXX_FLAGS_RELEASE=
	-DCMAKE_INSTALL_PREFIX=/home/ubuntu/.linuxbrew/Cellar/spades/3.5.0
	-DCMAKE_BUILD_TYPE=Release
	-DCMAKE_FIND_FRAMEWORK=LAST
	-DCMAKE_VERBOSE_MAKEFILE=ON