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Commit a5d359fd authored by Alexis CRISCUOLO's avatar Alexis CRISCUOLO
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wgetGenBankWGS.sh
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......@@ -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")";
......
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