arq5x

#!/usr/bin/env python
import sys
import pprint

def make_grantham_dict(grantham_mat_file):

        """
	Citation:   http://www.ncbi.nlm.nih.gov/pubmed/4843792
	Provenance: http://www.genome.jp/dbget-bin/www_bget?aaindex:GRAR740104

leipzig

#bin  chrom	chromStart	chromEnd	ix	n	size	type	bridge
0	chr1	124535434	142535434	1271	N	18000000	heterochromatin	no
23	chr1	121535434	124535434	1270	N	3000000	centromere	no
76	chr1	3845268	3995268	47	N	150000	contig	no
85	chr1	13219912	13319912	154	N	100000	contig	no
89	chr1	17125658	17175658	196	N	50000	clone	yes
101	chr1	29878082	30028082	337	N	150000	contig	no
188	chr1	120697156	120747156	1263	N	50000	clone	yes
188	chr1	120936695	121086695	1265	N	150000	contig	no
188	chr1	121485434	121535434	1269	N	50000	clone	no

ericminikel

#!/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/bin/Rscript

# Eric Vallabh Minikel
# CureFFI.org
# 2014-01-14
# example of how to use optparse in R scripts

# usage: ./exampleRScript1.r -a thisisa -b hiagain
#        ./exampleRScript1.r --avar thisisa --bvar hiagain

arq5x

dad	mom	kid	Inheritance description
HOM_REF	HOM_REF	HOM_REF	Expected
HOM_REF	HOM_REF	HET	Mendelian violation (plausible de novo)
HOM_REF	HOM_REF	HOM_ALT	Mendelian violation (implausible de novo)
HOM_REF	HOM_ALT	HOM_REF	Mendelian violation (uniparental disomy)
HOM_REF	HOM_ALT	HET	Expected
HOM_REF	HOM_ALT	HOM_ALT	Mendelian violation (uniparental disomy)
HOM_REF	HET	HOM_REF	Expected
HOM_REF	HET	HET	Expected

peterklipfel

sudo apt-get update
sudo apt-get install -y openjdk-7-jdk
sudo su -c 'echo "JAVA_HOME=\"/usr/lib/jvm/java-7-openjdk-amd64\"" >> /etc/environment'
cd /opt
sudo wget http://d3kbcqa49mib13.cloudfront.net/spark-1.0.1-bin-hadoop2.tgz
sudo tar -zxf spark-1.0.1-bin-hadoop2.tgz
cd spark-1.0.1-bin-hadoop2
# assumes that hostname is set correctly, and the main interface is on eth0, add HOSTNAME to /etc/hosts
sudo su -c "echo `ifconfig eth0 2>/dev/null|awk '/inet addr:/ {print $2}'|sed 's/addr://'` `cat /etc/hostname` >> /etc/hosts"
sbin/start-master.sh

arq5x

# assumes you have SSH'ed and qlogin'ed
cd thu
cd mydata

# slide 5
curl https://s3.amazonaws.com/gemini-tutorials/trio.trim.vep.vcf.gz > trio.trim.vep.vcf.gz
curl https://s3.amazonaws.com/gemini-tutorials/dominant.ped > dominant.ped
gemini load --cores 2 \
              -v trio.trim.vep.vcf.gz \
              -t VEP \

tomhopper

#' When plotting multiple data series that share a common x axis but different y axes,
#' we can just plot each graph separately. This suffers from the drawback that the shared axis will typically
#' not align across graphs due to different plot margins.
#' One easy solution is to reshape2::melt() the data and use ggplot2's facet_grid() mapping. However, there is
#' no way to label individual y axes.
#' facet_grid() and facet_wrap() were designed to plot small multiples, where both x- and y-axis ranges are
#' shared acros all plots in the facetting. While the facet_ calls allow us to use different scales with
#' the \code{scales = "free"} argument, they should not be used this way.
#' A more robust approach is to the grid package grid.draw(), rbind() and ggplotGrob() to create a grid of 
#' individual plots where the plot axes are properly aligned within the grid.

sterding

## data input (number of reads mapped to each category)
total=100
rRNA=5 # mapped to nuclear rRNA regions
mtRNA=7  # mapped to mitochondria genome
# for the rest of above, then we divide into different category, like http://www.biomedcentral.com/1741-7007/8/149 did.
intergenic=48 
introns=12
exons=30
upstream=3
downstream=6

mblondel

"""
Multiclass SVMs (Crammer-Singer formulation).

A pure Python re-implementation of:

Large-scale Multiclass Support Vector Machine Training via Euclidean Projection onto the Simplex.
Mathieu Blondel, Akinori Fujino, and Naonori Ueda.
ICPR 2014.
http://www.mblondel.org/publications/mblondel-icpr2014.pdf
"""

slowkow

#!/usr/bin/env bash
# bigWigRegions
# Kamil Slowikowski
#
# Depends on bigWigToBedGraph: http://hgdownload.cse.ucsc.edu/admin/exe/

if [[ $# -ne 2 ]]; then
    echo "bigWigRegions - Print bigWig data for each region in a bed file."
    echo -e "usage:\n   bigWigRegions in.bigWig in.bed > out.bedGraph"
    echo "   bigWigRegions in.bigWig <(zcat in.bed.gz) > out.bedGraph"