Entering edit mode
5.6 years ago
bgold04
•
0
Hi,
I am having trouble getting the below to work. The standard outs I am getting from the command line are at the bottom, as is the smallarray.txt test file. I think it is a syntax thing... but I would be much obliged for your constructive comments:
#! /bin/bash
# To make a library of PATRIC .fna sequences
cd /Users/bgold/Documents/PATRIC/
declare -a array
array=$(<smallarray.txt)
HOST='ftp.patricbrc.org'
USER='anonymous'
PASSWD='redacted@gmail.com'
#iterative part
for i in `seq 0 3`; do
VARIABLE=$i
FOLDER=${array["$VARIABLE"]}
FILE=${array["$VARIABLE"]}.fna
ftp --no-login $HOST <<END_SCRIPT
quote USER $USER
quote PASS $PASSWD
cd /patric2/patric3/genomes
cd $FOLDER
get $FILE
quit
END_SCRIPT
exit 0
done
##commented small array below
#####smallarray.txt########
##9.107
##9.108
##9.109
##9.11
###command line complaint from my Mac
#Berts-MacBook-Pro:PATRIC bgold$ ./experimentalscript.sh
#?Invalid command
#?Invalid command
#?Invalid command
#9.107: No such file or directory
#?Invalid command
#?Invalid command
#?Invalid command
