assign_taxonomy_nt.sh

#!/bin/bash

# Assigns taxonomy to nt blast searches, using the program ete3 and a script from David Ryder (originally LookupTaxonoDetails.py)

# Needs ete3 being installed, folder .etetoolkit/taxa.sqlite being present in the home directory, and script LookupTaxonDetails3.py being in path

# If folder .etetoolkit/taxa.sqlite is not present in home directory, you need to run ONLY the ete3 command once first, delete the output, and then set the third parameter to the .etetoolit/taxa.sqlite folder that has now been generated in your folder


usage="$(basename "$0") -b <blast_file> -c <n> -e <path/to/.etetoolkit/taxa.sqlite>

Usage:
	-b  Blast file including column with staxids
	-c  Number of the column containing staxids
	-e  Path to ~/.etetoolkit/taxa.sqlite
	-h  Display this help and exit"


# Set specified options
while getopts ':b:c:e:h' opt; do
  case "${opt}" in
  	b) blast_file="${OPTARG}" ;;
    c) column="${OPTARG}" ;;
    e) etetoolkit="${OPTARG}" ;;
	h) echo "$usage"
	   exit ;;
	:) printf "Option -$OPTARG requires an argument."
	   echo -e "\n$usage"
	   exit ;;
   \?) printf "Invalid option: -$OPTARG"
	   echo -e "\n$usage"
	   exit 
  esac
done
shift $((OPTIND - 1))


# Check if required options are set
if [[ -z "$blast_file" || -z "$column" || -z "$etetoolkit" ]]
then
   echo -e "-b, -c, and -e must be set.\n"
   echo -e "$usage\n\n"
   echo -e "Exiting script.\n"
   exit
fi


# Run script
blast_file_out_tmp=${blast_file%.*}_with_taxonomy.txt
blast_file_out=$(echo ${blast_file_out_tmp##*/}) # Creating variable so that output is saved in working directory
ete3 ncbiquery --info --search $(cut -f $column $blast_file) > matching_lineages.tsv
LookupTaxonDetails3.py -b $blast_file -l matching_lineages.tsv -o $blast_file_out -t $column -e $etetoolkit
echo 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxid lowest_rank lowest_hit superkingdom kingdom phylum subphylum class subclass order suborder infraorder family genus'| sed -e 's/ /\t/g' | cat - $blast_file_out > temp2 && mv temp2 $blast_file_out

rm matching_lineages.tsv