Bash to append array value to file before copying

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# 15  
Old 10-18-2019
Directory structure:
/path/to/${ID}*/path/to/folder (always this format)

The ${ID} will always be unique and have some random text after it that the * is used for. At the last folder in the path there is a .png always named cn_results that I am trying to append the unique ${ID} on front of ${ID}-cn_results.png, then scp that .png to${ID}-cn_results.png)

There are two values in array, but only the first is printed:

# Set an array in one step in bash
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list | tr -d '\r') )  ## match run with samples
echo "This is array" "$array" > /tmp/out

Contents of out
This is array ID1

I added a loop to iterate though each ID in array, but only the second value is printed:
# Set an array in one step in bash
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' "$run_dir"/rna.barcodes | tr -d '\r') )  ## match run with samples
   for file in "${array[@]}" ; do
    echo "This is array" "$file" > /tmp/loop.out

Contents of loop.out
This is array ID2

In this example array has two values in it ID1 and ID2, but there may be more or less it just depends on the run which the values for array come from. Thank you very much Smilie

Last edited by cmccabe; 10-18-2019 at 11:54 AM.. Reason: fixed format
# 16  
Old 10-18-2019
Show your actual directory structure EXPLICITLY, like
tree -d
├── D1
│   ├── D2
│   │   └── L1
│   ├── D3
│   │   └── L2
│   └── D4
│       ├── L1
│       ├── L2
│       └── L3
└── test
    └── D1
        └── D3
            ├── L1
            └── L2

14 directories

If your system doesn't have tree, use e.g. an editor to compose it.
This User Gave Thanks to RudiC For This Post:
# 17  
Old 10-18-2019
Hopefully this is better. Thank you Smilie.

│   ├── ${ID}*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID/folder
│   ├── ${ID}*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID/folder

# 18  
Old 10-18-2019
No, it's not. How do you expect people to bug hunt if they don't see what is actually going wrong? Show the directory listing from your target system. If that is confidential, build a dummy one but adapt your code to reproduce the error.
This User Gave Thanks to RudiC For This Post:
# 19  
Old 10-18-2019
Hopefully, this is better and helps:
# Set run array
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list | tr -d '\r') )  ## match run in rna.barcode and extract patient

# iterate through array
for ID in "${array[*]}" ; do
echo "$ID" > /tmp/out.txt
       echo "( cd /path/to/${ID}*/path/to/folder && xec sshpass -f file.txt scp -- *.png*${ID}-cn_results)"
       sshpass -f out.txt ssh -o strictHostKeyChecking=no -t xxx@xxx.xx.xx.xx

Contents of out --- This is array with all samples one one line ---

echo to terminal
( cd /path/to/ID1 ID2*/*/path/to/folder && exec sshpass -f file.txt scp -- *.png* ID2-cn_results.png)

├──/path/to/   ---- common path after ssh ---
│   ├── ID1*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID1/folder
│   ├── ID2*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID2/folder

After ssh to the common path on the server, each unique ID is used to further navigate to folder. In each folder there is a png (cn_results), that the unique ID is append to (ID-cn_results) and this 
append file is scp to It seems that since array is one line both are being used and that is causing the error?

# 20  
Old 10-18-2019
Well that's not going to work. You're just printing the statements to the screen and not giving anything to sshpass at all.

Does your script change the variable IFS? Strings are supposed to split when you do ARRAY=( 1 2 3 ) and not doing so is very weird unless IFS was changed.

That's why you need to be careful to do




...whenever you alter IFS for anything. If you don't put it back when you're done, that changes how all splitting works later.
This User Gave Thanks to Corona688 For This Post:
# 21  
Old 10-22-2019
I only printed the array to see what values were there and didn't change IFS (I don't think anyway). Thank you Smilie.
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