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Commit 3183ede3 authored by Alexis CRISCUOLO's avatar Alexis CRISCUOLO :black_circle:
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4.2

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wgetENAHTS.sh
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......@@ -4,7 +4,7 @@
# #
# wgetENAHTS: downloading HTS files from ENA #
# #
COPYRIGHT="Copyright (C) 2021-2022 Institut Pasteur" #
COPYRIGHT="Copyright (C) 2021-2023 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 #
......@@ -17,12 +17,13 @@
# You should have received a copy of the GNU General Public License along with this program. If not, see #
# <http://www.gnu.org/licenses/>. #
# #
# Contact: #
# 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 #
# Julien Guglielmini julien.guglielmini@pasteur.fr #
# Genome Informatics & Phylogenetics (GIPhy) giphy.pasteur.fr #
# Bioinformatics and Biostatistics Hub research.pasteur.fr/team/bioinformatics-and-biostatistics-hub #
# Dpt. Biologie Computationnelle research.pasteur.fr/department/computational-biology #
# Bioinformatics and Biostatistics Hub research.pasteur.fr/team/bioinformatics-and-biostatistics-hub #
# Dpt. Biologie Computationnelle research.pasteur.fr/department/computational-biology #
# Institut Pasteur, Paris, FRANCE research.pasteur.fr #
# #
##############################################################################################################
......@@ -33,7 +34,10 @@
# = VERSIONS = #
# ============ #
# #
VERSION=4.1.220307acjg #
VERSION=4.2.231202acjg #
# + fixed bug to the modified file report format #
# #
# VERSION=4.1.220307acjg #
# + fixed bugs with option -p #
# #
# VERSION=4.0.211129acjg #
......@@ -344,11 +348,13 @@ do
sleep 0.1 &>/dev/null ;
let DL++;
echo -n "." ;
while true; do $WGET_READ "$FILE_REPORT$ACCN" 2>&1 && break; done | sed -n '$p' | cut -f2-4 | tr '\t' '\n' > $OUTDIR/$ACCN.weh ;
# file report cols: 1 2 3 4 5 6 7 8 9 10 11 12
# f fastq_ftp fastq_bytes fastq_md5 bam_ftp bam_bytes bam_md5 submitted_ftp submitted_bytes submitted_md5 sra_ftp sra_bytes sra_md5 run_accession
while true; do $WGET_READ "$FILE_REPORT$ACCN" 2>&1 && break; done | sed -n '$p' | cut -f1-3 | tr '\t' '\n' > $OUTDIR/$ACCN.weh ;
echo -n "." ;
if [ ! -s $OUTDIR/$ACCN.weh ]
then
while true; do $WGET_READ "$FILE_REPORT$ACCN" 2>&1 && break; done | sed -n '$p' | cut -f2-4 | tr '\t' '\n' > $OUTDIR/$ACCN.weh ;
while true; do $WGET_READ "$FILE_REPORT$ACCN" 2>&1 && break; done | sed -n '$p' | cut -f1-3 | tr '\t' '\n' > $OUTDIR/$ACCN.weh ;
echo -n "." ;
fi
if [ ! -s $OUTDIR/$ACCN.weh ]
......
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