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3
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1 #!/bin/bash
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2 # Download/update RefSeq complete genomes
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3 echo "#### Updating RefSeq complete $1 genomes"
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4 wget -cNrv -t 45 -A *.gbk,*.fna "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/$1*" -P .
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5 # Download/update RefSeq draft genomes
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6 echo "#### Updating RefSeq draft $1 genomes"
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7 wget -cNrv -t 45 -A *.gbk.tgz,*.fna.tgz "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria_DRAFT/$1*" -P .
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8 # Download/update GenBank complete genomes
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9 echo "#### Updating GenBank complete $1 genomes"
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10 wget -cNrv -t 45 -A *.gbk,*.fna "ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/$1*" -P .
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11 # Download/update GenBank draft genomes
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12 echo "#### Updating GenBank draft $1 genomes"
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13 wget -cNrv -t 45 -A *.gbk.tgz,*.fna.tgz "ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria_DRAFT/$1*" -P .
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14 # Run script 'ncbi_concat_unpack.pl' to fill the result folders './refseq' and './genbank'
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15 echo "#### Copying files to result folder './refseq'"
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16 perl ncbi_ftp_concat_unpack.pl refseq y
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17 echo "#### Copying files to result folder './genbank'"
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18 perl ncbi_ftp_concat_unpack.pl genbank y
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