library(SRAdb)
sqlfile <- "~/ncbi/sradb/SRAmetadb.sqlite"
if(!file.exists("~/ncbi/sradb/SRAmetadb.sqlite")) sqlfile <<- getSRAdbFile(destdir = "~/ncbi/sradb")
file.info(sqlfile)
# sra_tables <- dbListTables(sra_con)
sra_con <- dbConnect(SQLite(),sqlfile)
rs <- getSRAinfo(c("SRP058527"), sra_con, sraType = "sra" )
sra_ids <- listSRAfile("SRP058527", sra_con)
check_sra <- function(sra_id)
{
sra_file <- paste0("~/ncbi/sradb/SRP058527/", sra_id, ".sra")
return(file.exists(sra_file))
}
if(!all(sapply(sra_ids$run, check_sra))) {
getSRAfile('SRP058527', sra_con, fileType='sra', destDir = "~/ncbi/sradb/SRP058527")
}
sra_paths <- list.files("~/ncbi/sradb/SRP058527", full.names = TRUE)
dump_fastq <- function(path)
{
system(paste("~/ncbi/sratoolkit.2.8.2-1-mac64/bin/fastq-dump",
"-O ~/ncbi/sradb/SRP058527_FASTQ/",
path))
}
sapply(sra_paths, dump_fastq)
### Metadata downloaded manually from https://www.ncbi.nlm.nih.gov/Traces/study/
### Lyrata transcriptome and proteome downloaded from
### ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Arabidopsis_lyrata/all_assembly_versions/GCF_000004255.1_v.1.0/GCF_000004255.1_v.1.0_rna.fna.gz
### ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Arabidopsis_lyrata/all_assembly_versions/GCF_000004255.1_v.1.0/GCF_000004255.1_v.1.0_protein.faa.gz
### ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Arabidopsis_lyrata/all_assembly_versions/GCF_000004255.1_v.1.0/GCF_000004255.1_v.1.0_feature_table.txt.gz
### Arabidopsis transcriptome downloaded from
### ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Arabidopsis_thaliana/latest_assembly_versions/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_protein.faa.gz
### ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Arabidopsis_thaliana/latest_assembly_versions/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_rna.fna.gz
### ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Arabidopsis_thaliana/latest_assembly_versions/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_feature_table.txt.gz
### index generation for lyrata -----------------------------------------------------------------
# #!bin/bash
#
# ## make index
# ./Salmon-0.7.2_linux_x86_64/bin/salmon\
# index -t GCF_000004255.1_v.1.0_rna.fna\
# -i al_transcripts_index\
# --type quasi -k 31
### index generation for thaliana -----------------------------------------------------------------
# #!bin/bash
#
# ## make index
# ./Salmon-0.7.2_linux_x86_64/bin/salmon\
# index -t GCF_000001735.3_TAIR10_rna.fna\
# -i at_transcripts_index\
# --type quasi -k 31
### Mapping for lyrata -----------------------------------------------------------------
# #!bin/bash
#
#
# for f in lyrata/*.fastq; do
#
# base=${f%.fastq}
# echo $base
# base=${base#lyrata/}
# echo $base
#
# ./Salmon-0.7.2_linux_x86_64/bin/salmon quant \
# -i al_transcripts_index -l U \
# -r $f -o $base\
# -p 8
# done
### Mapping for thaliana -----------------------------------------------------------------
# #!bin/bash
#
#
# for f in thaliana/*.fastq; do
#
# base=${f%.fastq}
# echo $base
# base=${base#thaliana/}
# echo $base
#
# ./Salmon-0.7.2_linux_x86_64/bin/salmon quant \
# -i at_transcripts_index -l U \
# -r $f -o $base\
# -p 8
# done
### Make orthogroups -----------------------------------------------------------------
# #!/bin/bash
#
# python OrthoFinder-master/orthofinder.py -f lyrata/orthogroups -t 3
#
# python OrthoFinder-master/orthofinder.py -b ~/lyrata/orthogroups/Results_Apr03/WorkingDirectory
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