I am trying to use a java script/software that is run by doing:
java -jar picard.jar MergeSamFiles \
I=input_1.bam \
I=input_2.bam \
O=output_merged_files.bam
where I= represents the input into the program. I have a text file with inputs that I would like to feed into this program, such as:
arg1
arg2
arg3
...
where each line gets converted into I=arg1 I=arg2 I=arg3 .... Is there an easy way to do this in bash?
I suggest to use an array:
# read file.txt to array
mapfile -t array < file.txt
# prefix every array element with "I="
java -jar picard.jar MergeSamFiles \
"${array[@]/#/I=}" \
O=output_merged_files.bam
In plain bash:
java -jar picard.jar MergeSamFiles \
$(IFS=$'\n'; printf "I=%s " $(<inputfile)) \
O=output_merged_files.bam
or alternatively
java -jar picard.jar MergeSamFiles \
$(while read -r; do echo "I=$REPLY"; done < inputfile) \
O=output_merged_files.bam
or using sed:
java -jar picard.jar MergeSamFiles \
$(sed 's/^/I=/' inputfile) \
O=output_merged_files.bam
I think something like this might work:
java -jar picard.jar MergeSamFiles $(sed -E 's/^/I=/' make_it_so.txt | xargs) O=output_merged_files.bam
If your input file has more args in it than xargs can flatten, you might run into some problems with the above.
