dwinter
/ rentrez_tutorial_draft.Rmd
Last active
August 29, 2015 14:01
— forked from sckott/rentrez_tutorial_draft.Rmd
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| --- | |
| title: rentrez tutorial | |
| layout: tutorial | |
| packge_version: 0.2.1 | |
| --- | |
| ```{r, eval=TRUE, echo=FALSE} | |
| opts_chunk$set(fig.path="../assets/tutorial-images/rentrez/") | |
| ``` |
dwinter
/ sra_fetch.py
Created
April 30, 2014 23:39
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| #!/usr/bin/env python | |
| """ | |
| Fetch all FASTQ files associated with an SRA ID | |
| usage: | |
| sra_fetch.py [sra-id] | |
| """ |
dwinter
/ make_artifact_bams
Created
April 22, 2014 19:31
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:98f1acba9791082035860796ccf52294670282ba8deb7745219206b5182498d8" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ |
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| gb_acc <- "JF493405" | |
| nuc_id <- entrez_search(db="nuccore", term=paste(gb_acc, "[accn]", sep=""))$id | |
| tax_links <- entrez_link(db="taxonomy", dbfrom="nuccore", id=nuc_id) | |
| tax_summ <- entrez_summary(db="taxonomy", id=tax_links$nuccore_taxonomy) |
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| library(stringr) | |
| library(rjson) | |
| geocode <- function(loc_string){ | |
| clean_loc <- str_replace_all(str_replace_all(loc_string, "[[:punct:]]", ""), " ", "+") | |
| base_url <- "http://maps.googleapis.com/maps/api/geocode/json?address=" | |
| loc_url <- paste(base_url, clean_loc, "&sensor=false", sep="") | |
| geocode <- fromJSON(paste(readLines(loc_url), collapse="")) | |
| if( length(geocode$results) > 0 ){ | |
| return(geocode$results[[1]]$geometry$location) |
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| library(rentrez) #written for devel-version on github | |
| fetch_abstract <- function(doi){ | |
| search <- entrez_search(term=paste(doi, "[doi]", sep=""), db="pubmed") | |
| rec <- parse_pubmed_xml(entrez_fetch(db="pubmed", id=search$ids, rettype="xml")) | |
| return(rec$abstract) | |
| } | |
| fetch_abstract("10.1111/j.1461-0248.2010.01509.x") |
dwinter
/ simulate_reads.py
Last active
December 18, 2015 22:39
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| import random | |
| def shotgun(iterable, size=12): | |
| """ """ | |
| start = random.choice(range(0, len(iterable)-size)) | |
| return(start, iterable[start:start+size]) | |
| def paired_end(iterable, read_size=10, gap_size=15): | |
| """ """ | |
| start = random.choice(range(0, len(iterable)-(read_size+gap_size))) |
dwinter
/ region_plot
Created
June 16, 2013 06:34
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| f <- function(x,y) sin(x)/cos(y) | |
| x <- seq(-5,5,0.1) | |
| y <- seq(-5,5,0.1) | |
| df <- expand.grid(x,y) #all possible combinations of x and y | |
| df$value <- apply(df, 1, function(x) f(x[1], x[2])) | |
| p <- ggplot(df, aes(Var1,Var2,fill=res>0)) | |
| p + geom_raster() |
dwinter
/ MCMCglmm_diag.r
Created
May 24, 2013 03:57
Quckly run a bunch of diagnostic tests on a list of MCMC runs
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| model_diagnostics <- function(modlist, plot=TRUE){ | |
| get_param_ranges <- function(x) { | |
| res <- apply((sapply(x, posterior.mode)),1,range) | |
| rownames(res) <- c("min", "max") | |
| return(res) | |
| } | |
| n <- length(modlist) | |
| on.exit(devAskNewPage(devAskNewPage())) #ie send it back the way it was |
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| df1 <- data.frame(x=sample(letters, 20), y=rnorm(20)) | |
| df2 <- data.frame(x=sample(letters, 20), z=rnorm(20)) | |
| new_df <- merge(df1, df2, all.x=TRUE) | |
| matched <- merged[complete.cases(merged),] | |
| unmatched <- merged[!complete.cases(merged),] |