INNER CODE UNIT · Shell
deleted_files
pirovc/genome_updater · genome_updater.sh:854
deleted_files=$((deleted_files + 1))
done <<<"${filelist}"
echo ${deleted_files}
}
check_missing_files()
{ # ${1} file, ${2} fields [assembly_accesion,url], ${3} extension - returns assembly accession, url and filename
join -1 3 -2 1 <(list_files "${1}" "${2}" "${3}" | sort -k 3,3 -t$'\t') <(list_local_files "${target_output_prefix}" | sort) -t$'\t' -v 1 -o "1.1,1.2,1.3"
}
check_complete_record()
{ # parameters: ${1} file, ${2} field [assembly accession, url], ${3} extension - returns assembly accession, url
expected_files=$(list_files "${1}" "${2}" "${3}" | sort -k 3,3)
join -1 3 -2 1 <(echo "${expected_files}" | sort -k 3,3) <(list_local_files "${target_output_prefix}" | sort) -t$'\t' -o "1.1" -v 1 | sort | uniq \
|
# Check for accessions with at least one missing file
join -1 1 -2 1 <(echo "${expected_files}" | cut -f 1,2 | sort | uniq) - -t$'\t' -v 1 # Extract just assembly accession and url for complete entries (no missing files)
}