Bash - pass argument from array

Question

I am using bash to call tool written in java (gatk) and I need to pass multiple arguments from array as input arguments. I tried it this way, but it seems not working. Could you please help me, how to solve it?

Code:

java $GATK \
    -T GenotypeGVCFs  \
    -R $ref \
    -o output.vcf \
    for foo in array
    do
        --variant  $foo \
    done

What i want to be called:

java $GATK \
    -T GenotypeGVCFs  \
    -R $ref \
    -o output.vcf \
    for foo in array
    do
        --variant  file1 \
        --variant  file2 \
        --variant  file3 ...etc
    done

edit: sorry for misunderstandings

array=("file1","file2","file3"...)

Thanks

You can't just throw a for inside another command. It doesn't evaluate to an expression. You get an actual for foo in array do... in your command line. — RealSkeptic
– RealSkeptic, Commented Jun 20, 2017 at 12:13
edited - array=("file1","file2","file3"...) @RealSkeptic - yea I know this doesnt work, so I am looking for solution how to pass into command multiple arguments from array :) — stanedav
– stanedav, Commented Jun 20, 2017 at 12:34

chepner · Accepted Answer · 2017-06-20 13:15:07Z

5

I assume that what you actually want is that if array contains a b c, to have the command

java $GATK \
    -T GenotypeGVCFs  \
    -R $ref \
    -o output.vcf \
    --variant a --variant b --variant c

If that is so, you can prepare a second array:

array=("file 1" "file 2" "file 3")
declare -a fullarray
for i in "${array[@]}"
do
    fullarray+=( --variant "$i" )
done

And then

java $GATK \
    -T GenotypeGVCFs  \
    -R $ref \
    -o output.vcf \
    "${fullarray[@]}"

This will also make sure that if any of the names in array contains a space, it will still be passed as a proper parameter and not split into two (assuming that you didn't mess it up when you added it to the array).

edited Jun 20, 2017 at 13:15

chepner

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answered Jun 20, 2017 at 12:49

RealSkeptic

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3 Comments

wich Over a year ago

quoting fullarray like that will pass "--variant a" as a single argument instead of as "--variant" and "a" separately, which will probably not work as intended

RealSkeptic Over a year ago

@wich Why do you think that? It expands each parameter in the array as a separate word.

wich Over a year ago

Ah indeed, my mistake, I thought you were changing the strings, not the arrays.

Tamar · Accepted Answer · 2017-06-20 12:46:20Z

0

With echo and $():

array=(file1 file2 file3)
java $GATK \
    -T GenotypeGVCFs  \
    -R $ref \
    -o output.vcf \
    $(for foo in ${array[*]}
    do
        echo -n " --variant  $foo"
    done)

answered Jun 20, 2017 at 12:46

Tamar

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1 Comment

chepner Over a year ago

No; this negates any advantage using an array in the first place would provide.

wich · Accepted Answer · 2017-06-20 12:56:02Z

0

You can do this with the following:

java $GATK \
    -T GenotypeGVCFs  \
    -R $ref \
    -o output.vcf \
    ${array[*]/#/ --variant }

edited Jun 20, 2017 at 12:56

answered Jun 20, 2017 at 12:53

wich

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2 Comments

RealSkeptic Over a year ago

What about possible spaces in the file names?

wich Over a year ago

@RealSkeptic OP didn't bother about spaces so I didn't either

glenn jackman · Accepted Answer · 2017-06-20 14:29:45Z

0

@RealSkeptic's answer is the best. I'd write, for readability:

array=( "file 1" "file 2" "file 3" )
args=(
    "$GATK"
    -T GenotypeGVCFs 
    -R "$ref"
    -o output.vcf
)
for foo in "${array[@]}"; do args+=( --variant "$foo" ); done

java "${args[@]}"

answered Jun 20, 2017 at 14:29

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