update the download script

Author: XiaomingXu1995

benchmark/download/README.md

@@ -8,13 +8,12 @@ For the input of a single FASTA file (each sequence means a genome), RabbitTClus
 ## download genomes from RefSeq
 The download script comes from [Bonsai](https://github.com/dnbaker/bonsai/tree/ac6f8c7ee1b2ae1128970a8f6dc01ddad19fdb37).
 
-RefSeq bacterial genomes can be downloaded by `download_refseq.py` as follows:
+The latest release of RefSeq bacterial genomes can be downloaded by `download_refseq.py` as follows:
 
 * `python3 download_genomes.py bacteria`  
 * `python3 download_genomes.py -h` more details of help infos.
 
 ## download genomes from GenBank
-The FTP paths of the GenBank assembled bacterial genomes are listed in `bact_GenBank.list.gz`, which is generated from [assembly_summary_genbank.txt](https://ftp.ncbi.nlm.nih.gov/genomes/genbank/).
 
-GenBank bacterial genomes can be downloaded by `download_genbank.sh` as follows:
+The latest release of GenBank bacterial genomes can be downloaded by `download_genbank.sh` as follows:
 * `./download_genbank.sh`

benchmark/download/bact_GenBank.list.gz

@@ -1,15 +1,19 @@
 #!/bin/bash
+
+wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt
+awk -F '\t' 'NR>2 {print $20}' assembly_summary.txt >ftp.list
+
 outputDir="genbankDir"
 echo $#
 if [ $# -ge 1 ]
 then
 	outputDir=$1
 fi
 mkdir -p $outputDir
-zcat bact_GenBank.list.gz | while read -r line ; 
+cat ftp.list | while read line
 do
-    fname=$(echo $line | grep -o 'GCA_.*' | sed 's/$/_genomic.fna.gz/') ;
-    #echo "$line/$fname" ;
+    fname=$(echo $line | grep -o 'GCA_.*' | sed 's/$/_genomic.fna.gz/')
+    #echo "$line/$fname"
     wget -c "$line/$fname" ;
 		mv "$fname" $outputDir
 done