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Commit d8275ce4 authored by Alexis CRISCUOLO's avatar Alexis CRISCUOLO :black_circle:
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0.7

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README.md
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......@@ -30,11 +30,11 @@ Run _wgetGenBankWGS_ with the following command line model:
Run _wgetGenBankWGS_ without option to read the following documentation:
```
wgetGenBankWGS Copyright (C) 2019-2021 Institut Pasteur
wgetGenBankWGS Copyright (C) 2019-2021 Institut Pasteur
Downloading sequence files corresponding to selected entries from genome assembly report files:
GenBank: ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt
RefSeq: ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt
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
RefSeq: ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt
Selected entries (options -e and -v) can be restricted to a specific phylum using option -p:
-p A archaea
......
wgetGenBankWGS.sh
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......@@ -33,7 +33,10 @@
# = VERSIONS = #
# ============ #
# #
VERSION=0.6.201018ac #
VERSION=0.7.211026ac #
# + takes into account the new protocol https in field ftp_path of the genome assembly report files #
# #
# VERSION=0.6.211018ac #
# + takes into account the last field 'asm_not_live_date' in genome assembly report files #
# + adding option -p to select a specific phylum #
# #
......@@ -71,11 +74,11 @@ if [ "$1" = "-?" ] || [ "$1" = "-h" ] || [ $# -le 1 ]
then #
cat <<EOF
wgetGenBankWGS v.$VERSION Copyright (C) 2019-2021 Institut Pasteur
wgetGenBankWGS v.$VERSION Copyright (C) 2019-2021 Institut Pasteur
Downloading sequence files corresponding to selected entries from genome assembly report files:
GenBank: ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt
RefSeq: ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt
Downloading sequence files corresponding to selected entries from genome assembly report files (option -d):
GenBank: ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt
RefSeq: ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt
Selected entries (options -e and -v) can be restricted to a specific phylum using option -p:
-p A archaea
......@@ -151,6 +154,7 @@ fi
# =============== #
# #
# = PROTOCOL can be either "ftp:" or "https"; however, "https:" is generally faster ====================== #
# = however since Sep. 2021, the default protocol is now "https" ====================== #
# #
PROTOCOL="https:";
# #
......@@ -314,7 +318,7 @@ if [ "$EXCLUDE_PATTERN" != "^#" ]; then echo "exclusion criterion: $EXCLUDE_PATT
tmp=$(randomfile $SUMMARY);
mv $SUMMARY $tmp ;
sed -n '2p' $tmp > $SUMMARY ;
sed '1,2d' $tmp | grep -E "$INCLUDE_PATTERN" | grep -v -E "$EXCLUDE_PATTERN" | grep -F "ftp://ftp.ncbi.nlm.nih.gov" >> $SUMMARY ;
sed '1,2d' $tmp | grep -E "$INCLUDE_PATTERN" | grep -v -E "$EXCLUDE_PATTERN" | grep -F "ftp.ncbi.nlm.nih.gov" >> $SUMMARY ;
rm $tmp ;
n=$(grep -v -c "^#" $SUMMARY);
echo "$REPOSITORY: $n entries" ;
......
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