| // saving from url to a file (append) | |
| new File("output.xml") << new URL ("http://some.url/some/path.xml").getText() |
People
 :bowtie: |
😄 :smile: |
😆 :laughing: |
|---|---|---|
😊 :blush: |
😃 :smiley: |
:relaxed: |
😏 :smirk: |
😍 :heart_eyes: |
😘 :kissing_heart: |
😚 :kissing_closed_eyes: |
😳 :flushed: |
😌 :relieved: |
😆 :satisfied: |
😁 :grin: |
😉 :wink: |
😜 :stuck_out_tongue_winking_eye: |
😝 :stuck_out_tongue_closed_eyes: |
😀 :grinning: |
😗 :kissing: |
😙 :kissing_smiling_eyes: |
😛 :stuck_out_tongue: |
| #GATK Method <- Slower and keeps original ID plut dbSNP rsID | |
| # R=Reference FASTA | |
| # V=VCF file to add IDs to | |
| # --dbsnp = dbsnp VCF -- download from NCBI FTP | |
| java -jar GenomeAnalysisTK.jar -R /reference/Homo_sapiens_assembly19.fasta -T VariantAnnotator -V vcf_to_add_id_to.vcf --dbsnp /reference/dbsnp_137.b37.vcf.gz --out /data/Broad.chr1.annotated.vcf | |
| #bcftools Method <- Faster, replaces existing ID with dbSNP rsID | |
| /usr/bin/htslib/bcftools/bcftools annotate -a /reference/dbsnp_137.b37.vcf.gz -c ID vcf_to_add_id_to.vcf |
| # stack overflow answer from Joran Ellis: | |
| # http://stackoverflow.com/questions/5319839/read-multiple-csv-files-into-separate-data-frames | |
| # If the path is different than your working directory | |
| # you'll need to set full.names = TRUE to get the full | |
| # paths. | |
| my_files <- list.files("path/to/files") | |
| # Further arguments to read.csv can be passed in ... | |
| all_csv <- lapply(my_files,read.csv,...) |
UPDATE (March 2020, thanks @ic): I don't know the exact AMI version but yum install docker now works on the latest Amazon Linux 2. The instructions below may still be relevant depending on the vintage AMI you are using.
Amazon changed the install in Linux 2. One no-longer using 'yum' See: https://aws.amazon.com/amazon-linux-2/release-notes/
sudo amazon-linux-extras install docker
sudo service docker start
| ggroc <- function(roc, showAUC = TRUE, interval = 0.2, breaks = seq(0, 1, interval)){ | |
| require(pROC) | |
| if(class(roc) != "roc") | |
| simpleError("Please provide roc object from pROC package") | |
| plotx <- rev(roc$specificities) | |
| ploty <- rev(roc$sensitivities) | |
| ggplot(NULL, aes(x = plotx, y = ploty)) + | |
| geom_segment(aes(x = 0, y = 1, xend = 1,yend = 0), alpha = 0.5) + | |
| geom_step() + |
| #' Create a Kaplan-Meier plot using ggplot2 | |
| #' | |
| #' @param sfit: a survfit object | |
| #' @param table: logical: Create a table graphic below the K-M plot, indicating at-risk numbers? | |
| #' @param returns logical: if TRUE, return an arrangeGrob object | |
| #' @param xlabs: x-axis label | |
| #' @param ylabs: y-axis label | |
| #' @param ystratalabs: The strata labels. Default = levels(summary(sfit)$strata) | |
| #' @param ystrataname: The legend name. Default = "Strata" | |
| #' @param timeby numeric: control the granularity along the time-axis |
| import papermill as pm | |
| pm.execute_notebook('weather_forecast_using_pyowm.ipynb', | |
| 'weather_forecast_using_pyowm_output.ipynb', | |
| parameters={'city':'Sao Paulo,BR'}, | |
| kernel_name='papermill-tutorial') |
| params.directories="." | |
| params.headsize=100000 | |
| params.extensions="bam bai" | |
| params.help=false | |
| params.extrafind="" | |
| params.lines = 1000 | |
| params.publishDir="." | |
| def helpMessage() { | |
| log.info""" |
| library(flametree) | |
| library(ggplot2) | |
| library(gganimate) | |
| dat <- flametree_grow(time = 13) | |
| pic <- ggplot( | |
| data = dat, | |
| mapping = aes( | |
| x = coord_x, |
