Mercurial > repos > dereeper > pangenome_explorer
view COG/bac-genomics-scripts/ncbi_ftp_download/ncbi_ftp_download.sh @ 10:d103c41b6931 draft
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author | dereeper |
---|---|
date | Thu, 30 May 2024 16:35:22 +0000 |
parents | e42d30da7a74 |
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#!/bin/bash # Download/update RefSeq complete genomes echo "#### Updating RefSeq complete $1 genomes" wget -cNrv -t 45 -A *.gbk,*.fna "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/$1*" -P . # Download/update RefSeq draft genomes echo "#### Updating RefSeq draft $1 genomes" wget -cNrv -t 45 -A *.gbk.tgz,*.fna.tgz "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria_DRAFT/$1*" -P . # Download/update GenBank complete genomes echo "#### Updating GenBank complete $1 genomes" wget -cNrv -t 45 -A *.gbk,*.fna "ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/$1*" -P . # Download/update GenBank draft genomes echo "#### Updating GenBank draft $1 genomes" wget -cNrv -t 45 -A *.gbk.tgz,*.fna.tgz "ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria_DRAFT/$1*" -P . # Run script 'ncbi_concat_unpack.pl' to fill the result folders './refseq' and './genbank' echo "#### Copying files to result folder './refseq'" perl ncbi_ftp_concat_unpack.pl refseq y echo "#### Copying files to result folder './genbank'" perl ncbi_ftp_concat_unpack.pl genbank y