https://bioinformaticsonline.com/snippets/view/33321/download-the-genome-from-ncbi-using-bash-scriptcommand? https://bioinformaticsonline.com/snippets/view/33321/download-the-genome-from-ncbi-using-bash-scriptcommand Tue, 30 May 2017 08:11:33 -0500 https://bioinformaticsonline.com/snippets/view/33321/download-the-genome-from-ncbi-using-bash-scriptcommand #!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome # Look for genome assembly summary and extract the URL # USER need to provide the right summary file to curl # Commentline if you are not interested in that genome set # -for fungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_fungi # -for bacteria curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_bacteria # -for plant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_plant # -for archaea curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_archaea # -for protozoa curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_protozoa # -for vertebrate_mammalian curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_vertebrate_mammalian # -for vertebrate_other curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_vertebrate_other # -for invertebrate curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_invertebrate # -for viral curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_viral #Read the url from file and download FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." filename=$(basename "$f") extension="${filename##*.}" filename="${filename%.*}" # Create a directory with appending G mkdir "G$filename" cd "G$filename" # take action on each file. $f store current file name wget --input $f #cat $f cd .. done #Reference #ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_Downloading_Genomic_Data.pdf]]> Jit