diff --git a/wgetGenBankWGS.sh b/wgetGenBankWGS.sh index 820af93538f02cf85453c42b5aebf2abc70efa7e..a4323dede7f29c34576d39b975c7079ad861adb2 100755 --- a/wgetGenBankWGS.sh +++ b/wgetGenBankWGS.sh @@ -4,7 +4,7 @@ # # # wgetGenBankWGS: downloading WGS genome assembly files from NCBI # # # -# Copyright (C) 2019-2024 Institut Pasteur # + COPYRIGHT="Copyright (C) 2019-2025 Institut Pasteur" # # # # This program is free software: you can redistribute it and/or modify it under the terms of the GNU # # General Public License as published by the Free Software Foundation, either version 3 of the License, or # @@ -20,7 +20,7 @@ # Contact: # # Alexis Criscuolo alexis.criscuolo@pasteur.fr # # Genome Informatics & Phylogenetics (GIPhy) giphy.pasteur.fr # -# Centre de Ressources Biologiques de l'Institut Pasteur (CRBIP) research.pasteur.fr/en/b/VTq # +# Centre de Ressources Biologiques de l'Institut Pasteur (CRBIP) crbip.pasteur.fr # # Institut Pasteur, Paris, FRANCE research.pasteur.fr # # # # 4888888883 # @@ -47,7 +47,10 @@ # = VERSIONS = # # ============ # # # - VERSION=0.92-240423ac # + VERSION=0.93-250324ac # +# + simplified output file name for some type strains # +# # +# VERSION=0.92-240423ac # # + fixed bug in type strain selection # # + updated trap # # # @@ -102,7 +105,7 @@ if [ "$1" = "-?" ] || [ "$1" = "-h" ] || [ $# -le 1 ] then # cat <<EOF - wgetGenBankWGS v.$VERSION Copyright (C) 2019-2024 Institut Pasteur + wgetGenBankWGS v.$VERSION $COPYRIGHT Downloading sequence files corresponding to selected entries from genome assembly report files (option -d): GenBank: ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt @@ -408,12 +411,14 @@ do let i++; if [ $i -lt 1 ]; then continue; fi NAME=$(echo "$organism_name" | tr ",/\?%*:|'\"<>()[]#;" '_' | ### replacing special char. by '_' - sed -e 's/ bv\./ bv/;s/ genomosp\./ genomosp/;s/ sp\./ sp/;s/ str\./ str/;s/ subsp\./ subsp/'); + sed -e 's/ bv\./ bv/;s/ genomosp\./ genomosp/;s/ sp\./ sp/;s/ str\./ str/;s/ subsp\./ subsp/'); + PNAME="$NAME"; - STRAIN=$(echo "$infraspecific_name" | grep -v "^na$" | sed 's/strain=//g' | tr ",/\?%*:|'\"<>()[]#;" '_'); ### replacing special char. by '_' + STRAIN=$(echo "$infraspecific_name" | grep -v "^na$" | sed 's/type strain: //g;s/strain=//g' | tr ",/\?%*:|'\"<>()[]#;" '_'); ### replacing special char. by '_' [ -n "$STRAIN" ] && [ $(echo "$NAME" | grep -c -F "$STRAIN") -eq 0 ] && NAME="$NAME.$STRAIN"; ISOLATE=$(echo "$isolate" | grep -v "^na$" | tr ",/\?%*:|'\"<>()[]#;" '_'); ### replacing special char. by '_' + [ -n "$ISOLATE" ] && [ $(echo "$ISOLATE" | grep -c "$STRAIN") -ne 0 ] && NAME="$PNAME"; [ -n "$ISOLATE" ] && [ $(echo "$NAME" | grep -c -F "$ISOLATE") -eq 0 ] && NAME="$NAME.$ISOLATE"; TYPE_MATERIAL="$(grep -v "^na$" <<<"$relation_to_type_material")";