Mercurial > repos > dereeper > pangenome_explorer
diff COG/bac-genomics-scripts/ncbi_ftp_download/ncbi_ftp_download.sh @ 3:e42d30da7a74 draft
Uploaded
| author | dereeper |
|---|---|
| date | Thu, 30 May 2024 11:52:25 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COG/bac-genomics-scripts/ncbi_ftp_download/ncbi_ftp_download.sh Thu May 30 11:52:25 2024 +0000 @@ -0,0 +1,18 @@ +#!/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