seandavi

library(dplyr)


library(RMySQL)
con = dbConnect(MySQL(),user='USERNAME',password='PASSWORD',host='solexadb.XXXXXXXXXX.us-east-1.rds.amazonaws.com',port=3306,dbname='solexa')
res = dbGetQuery(con,
                 "select study_id,source.name as source_name, sample.name as sample_name, fcb.type as software,
                 fcb.dateStamp as basecalldate, fcb.softwareVersion as version, study_id,
                 sr.date as run_date, sr.sequencer as sequencer, sm.model, ssr.library_id as library_id,
                 sr.ID as run_id, sample.ID as sample_id, nt.value as sample_source,

seandavi

import boto3

# set the profile name based on ~/.aws/credentials entry
boto3.setup_default_session(profile_name='s3')

from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
s3 = S3RemoteProvider()

# This simply copies the file from local storage to s3
rule all:

seandavi

library(aws.s3)
aws.signature::use_credentials(profile='s3')
disco_maf = s3read_using(readr::read_tsv,object="s3://target-osteosarcoma/TargetOsteoDiscovery/summary/strelka.maf.filtered.tab")
disco_gistic = s3read_using(readr::read_tsv,object="s3://target-osteosarcoma/TargetOsteoDiscovery/all_thresholded.by_genes.txt")
library(tidyr)
library(dplyr)
library(ComplexHeatmap)
x = disco_gistic %>% 
  gather(key = 'Sample', value='CN', -c('Gene Symbol', "Locus ID", "Cytoband")) %>%
  dplyr::select(Sample, Hugo_Symbol = `Gene Symbol`, CN) %>%

seandavi

library(GenomicDataCommons)
library(magrittr)

TCGAtranslateID = function(file_ids) {
    info = files() %>%
        GenomicDataCommons::filter( ~ file_id %in% file_ids) %>%
        GenomicDataCommons::select('cases.samples.submitter_id') %>%
        results_all()
    # The mess of code below is to extract TCGA barcodes
    # id_list will contain a list (one item for each file_id)

seandavi

#!/usr/bin/env python
import argparse
import lxml.etree
import os, sys
import bz2

parser = argparse.ArgumentParser()
parser.add_argument('tag')
parser.add_argument('n',default=100000)
parser.add_argument('wrapper', default=None)

seandavi

# I often want to add new users
# to AWS machines in a semi-automated
# script, perhaps via SSH. Doing
# so noninteractively took some search
# work.

sudo useradd USERNAME
echo "USERNAME:NEWPASSWORD" | sudo chpasswd

seandavi

# Mine tweets from a meeting using the meeting hashtag.
# 
# Looks for URLs in tweets that match:
#   - github
#   - github pages (docs)
#   - bitbucket
#   - CRAN
#   - BitBucket
#
# Results in a tidy data.frame that can be further manipulated

seandavi

seandavi

sdavis2@Seans-MBP-3:~/Documents/git$ R CMD INSTALL SRA2R
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘SRA2R’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include "-I/usr/local/opt/openssl/include"   -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Users/sdavis2/include -I/Users/sdavis2/include  -I"/Library/Frameworks/R.framework/Ve

seandavi

#
# This is a Shiny web application. You can run the application by clicking
# the 'Run App' button above.
#
# Find out more about building applications with Shiny here:
#
#    http://shiny.rstudio.com/
#

library(shiny)