In Indicai-dev/kannarip:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

PAGE_BASE <- 'https://www.kannapedia.net/strains/page/'

STRAIN_BASE <- 'https://www.kannapedia.net/strains/'

http://mgcdata.s3.amazonaws.com/rsp_fastqs/RSP10012_CGATCTG_ALWYH/RSP10012_CGATCTG_L001_R1_001.fastq.gz

FASTA_BASE <- 'http://mgcdata.s3.amazonaws.com/rsp_fastqs/'

http://mgcdata.s3.amazonaws.com/analyses/RSP10012_ALWYH_20160810215959/RSP10012_ALWYH_2016081022001.vcf.gz.filtered.vcf

VCF_BASE <- 'http://mgcdata.s3.amazonaws.com/analyses/'

dbConn <- dbConnect( RSQLite::SQLite(), # Namespace loaded from kannarip system.file('kannapedia-genomes.sqlite', 'kannarip') )

# devtools::install_github('Indicai-dev/kannarip')

library(kannarip)
rip(1)

$RSP10100
[1] "pheno"

$RSP11350
[1] "pheno"  "vcf"    "fasta1" "fasta2"

$RSP11442
[1] "pheno"  "vcf"    "fasta1" "fasta2"

$RSP10156
[1] "pheno"  "vcf"    "fasta1" "fasta2"

$RSP10287
[1] "pheno"  "vcf"    "fasta1" "fasta2"

Indicai-dev/kannarip documentation built on Sept. 2, 2020, 12:36 p.m.