Benjamin Langmead BenLangmead
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| system('curl https://trace.ncbi.nlm.nih.gov/Traces/sra/sra_stat.cgi > /tmp/stats.csv') | |
| st <- read.table('/tmp/stats.csv', sep=',', header=T) | |
| st$date <- as.Date(st$date, format='%m/%d/%Y') | |
| i <- min(which(st$bases >= 0.5625e16)) | |
| id1 <- i | |
| id2 <- min(which(st$bases >= 1.125e16)) | |
| id3 <- min(which(st$bases >= 2.25e16)) | |
| id4 <- min(which(st$bases >= 4.5e16)) | |
| id5 <- min(which(st$bases >= 8.95e16)) | |
| plot(st$date[id1:id5], log10(st$bases[id1:id5]), type='l', xlab="Date", ylab="log10(Total SRA bases)") |
BenLangmead
/ sradbv2.py
Created
July 4, 2018 02:10
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| #!/usr/bin/env python | |
| # Authors: Chris Wilks (original) and Ben Langmead (modifications) | |
| # Date: 7/3/2018 | |
| # License: MIT | |
| """sradbv2 | |
| Usage: | |
| sradbv2 search <lucene-search> [options] | |
| sradbv2 query [<SRP>,<SRR>]... [options] |
BenLangmead
/ gist:f40ff161c3be517b5b4d8867479fe4ee
Created
June 2, 2018 21:01
gathering human rna-seq w/ sradbv2
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| > query=paste( | |
| + 'sample_taxon_id:9606', | |
| + 'experiment_library_strategy:"rna seq"', | |
| + 'experiment_library_source:transcriptomic', | |
| + 'experiment_platform:illumina') | |
| > st <- 0 | |
| > SZ <- 500 | |
| > df <- sra_full_search(q=query, start=st, size=SZ); st <- st + SZ | |
| https://api-omicidx.cancerdatasci.org/sra/1.0/search/full?q=sample_taxon_id%3A9606%20experiment_library_strategy%3A%22rna%20seq%22%20experiment_library_source%3Atranscriptomic%20experiment_platform%3Aillumina&start=0&size=500 | |
| > print(paste('ncol for batch', st, '=', ncol(df))) |
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| R version 3.5.0 (2018-04-23) -- "Joy in Playing" | |
| Copyright (C) 2018 The R Foundation for Statistical Computing | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| Natural language support but running in an English locale |
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| library('SRAdb') | |
| # If you have SRAmetadb already, set this directory, or setwd appropriately | |
| # to save yourself a large download | |
| sqlfile <- file.path('.', 'SRAmetadb.sqlite') | |
| if(!file.exists('SRAmetadb.sqlite')) sqlfile <<- getSRAdbFile() | |
| sra_con <- dbConnect(SQLite(),sqlfile) | |
| q <- function(x) { dbGetQuery(sra_con, x) } | |
| species_to_tax_id = list( |
BenLangmead
/ benchmarks.R
Last active
May 13, 2017 00:47
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| #!/usr/bin/env Rscript | |
| # source('http://bioconductor.org/biocLite.R') | |
| # bioClite('recount') | |
| # bioClite('GenomicRanges') | |
| # bioCLite('LieberInstitute/recount.bwtool') | |
| library('GenomicRanges') | |
| library('recount') | |
| library('recount.bwtool') |
BenLangmead
/ CG_Radix
Created
May 8, 2014 22:12
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| { | |
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| "signature": "sha256:0e059d6141a29e725dcfd5b05c7fa0fe7e20abcd0698fa34124a7c847f09627d" | |
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BenLangmead
/ FASTQ.json
Created
January 11, 2014 20:31
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| { | |
| "metadata": { | |
| "name": "" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
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BenLangmead
/ FASTA.json
Last active
January 2, 2016 12:59
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| { | |
| "metadata": { | |
| "name": "" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
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BenLangmead
/ CG_Naive.json
Created
January 4, 2014 18:42
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| { | |
| "metadata": { | |
| "name": "" | |
| }, | |
| "nbformat": 3, | |
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