bionode - Get all reads FASTQ for Solenopsis invicta assembly

bionode-fastq-solenopsis.sh

bionode-ncbi search genome Solenopsis invicta | tool-stream extractProperty assemblyid | bionode-ncbi search assembly - | tool-stream extractProperty uid | bionode-ncbi link assembly bioproject - | tool-stream extractProperty destUID | bionode-ncbi link bioproject sra - | tool-stream extractProperty destUID | bionode-ncbi search sra - | grep -e 20kb -e 8kb| tool-stream extractProperty uid24418

# Gives:
#23917
#23918
#23919
#23920
#23951
#23952
#23953


bionode-ncbi search genome Solenopsis invicta | tool-stream extractProperty assemblyid | bionode-ncbi search assembly - | tool-stream extractProperty uid | bionode-ncbi link assembly bioproject - | tool-stream extractProperty destUID | bionode-ncbi link bioproject sra - | tool-stream extractProperty destUID | bionode-ncbi search sra - | grep -e 20kb -e 8kb| tool-stream extractProperty uid | bionode-ncbi urls sra - | tool-stream extractProperty urlhttp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058742/SRR058742.sra

# Gives:
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058747/SRR058747.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058749/SRR058749.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058750/SRR058750.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058751/SRR058751.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058752/SRR058752.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058753/SRR058753.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059303/SRR059303.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059304/SRR059304.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059305/SRR059305.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059306/SRR059306.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059307/SRR059307.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059308/SRR059308.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059309/SRR059309.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059310/SRR059310.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059311/SRR059311.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059312/SRR059312.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059313/SRR059313.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR059/SRR059314/SRR059314.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058745/SRR058745.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058746/SRR058746.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058743/SRR058743.sra
#http://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR058/SRR058744/SRR058744.sra


bionode-ncbi search genome Solenopsis invicta | tool-stream extractProperty assemblyid | bionode-ncbi search assembly - | tool-stream extractProperty uid | bionode-ncbi link assembly bioproject - | tool-stream extractProperty destUID | bionode-ncbi link bioproject sra - | tool-stream extractProperty destUID | bionode-ncbi search sra - | grep -e 20kb -e 8kb| tool-stream extractProperty uid | bionode-ncbi download sra - | tool-stream collectMatch status completed | bionode-sra fastq-dump -

#Gives FASTQ files inside folders named using the UIDs