Error assigning bash command's output to variable with Julia

New to Julia
1

I would like to run a bash command called samtools and assign its output to a variable that I can process with julia. Thus I made:

julia> r_file
"A3-T_F-AlnSrtDed.bam"
julia> r_locus
"chrV:254748988-254749089"
julia> query = run(pipeline(`samtools ... $r_file $r_locus`,
                       `grep -v @`,  `cut -f 5`), String)
ERROR: MethodError: no method matching spawn_opts_inherit(::Type{String})
Closest candidates are:
  spawn_opts_inherit() at process.jl:545
  spawn_opts_inherit(::Tuple{Union{RawFD, FileRedirect, IO},Union{RawFD, FileRedirect, IO},Union{RawFD, FileRedirect, IO}}) at process.jl:541
  spawn_opts_inherit(::Union{RawFD, FileRedirect, IO}) at process.jl:545
  ...
Stacktrace:
 [1] #run#503(::Bool, ::Function, ::Base.OrCmds, ::Type) at ./process.jl:662
 [2] run(::Base.OrCmds, ::Type) at ./process.jl:661
 [3] top-level scope at none:0

julia> query = run(pipeline(`samtools ... $r_file $r_locus`, 
   `grep -v @`,  `cut -f 5`))
21
Base.ProcessChain(Base.Process[Process(`samtools ... A3-T_F-AlnSrtDed.bam chrV:254748988-254749089`, ProcessExited(0)), Process(`grep -v @`, ProcessExited(0)), Process(`cut -f 5`, ProcessExited(0))], RawFD(0x00000000), RawFD(0x00000001), RawFD(0x00000002))

Essentially, if I don’t use String, the command is assigned to query but without String I get an error.

What is the correct way to assign the shell’s output to a variable? This should be either a string (if there is a single output) or an array.

2

Are you looking for:

query = read(pipeline(`samtools ... $r_file $r_locus`,
                       `grep -v @`,  `cut -f 5`), String)
2 Likes
3

Yes I am, thank you