mirror of
https://github.com/metabarcoding/obitools4.git
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30 lines
684 B
Bash
Executable File
30 lines
684 B
Bash
Executable File
#!/bin/bash
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URL=https://ftp.ncbi.nlm.nih.gov/genbank/
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DIV="bct|inv|mam|phg|pln|pri|rod|vrl|vrt"
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GB_Release_Number=$(curl "${URL}GB_Release_Number")
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mkdir -p "Release-${GB_Release_Number}"
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cd "Release-${GB_Release_Number}"
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curl $URL > index.html
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for f in $(egrep "gb(${DIV})[0-9]+\.seq\.gz" index.html \
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| sed -E 's@^.*<a href="([^"]+)">.*</a>.*$@\1@' ) ; do
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echo -n "File : $f"
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if [[ -f $f ]] ; then
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gzip -t $f && echo " ok" || rm -f $f
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fi
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while [[ ! -f $f ]] ; do
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echo downloading
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wget2 --progress bar -v -o - $URL$f
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if [[ -f $f ]] ; then
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gzip -t $f && echo " ok" || rm -f $f
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fi
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done
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done
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