Scripts

MIToS implements several useful scripts to command line execution (without requiring Julia coding). All this scripts are located in the scripts folder of the MIToS directory. You can copy them to your working directory, use the path to their folder or put them in the path (look into the Installation section of this manual).

• Scripts
• Buslje09.jl
• BLMI.jl
• Conservation.jl
• DownloadPDB.jl
• Distances.jl
• MSADescription.jl
• PercentIdentity.jl
• AlignedColumns.jl
• SplitStockholm.jl

Buslje09.jl

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Buslje09.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/Buslje09.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package MIToS not found in current path:
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/Buslje09.jl:7
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/Buslje09.jl -h`, ProcessExited(1)) [1]

BLMI.jl

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "BLMI.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/BLMI.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package MIToS not found in current path:
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/BLMI.jl:7
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/BLMI.jl -h`, ProcessExited(1)) [1]

Conservation.jl

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Conservation.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/Conservation.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package MIToS not found in current path:
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/Conservation.jl:6
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/Conservation.jl -h`, ProcessExited(1)) [1]

DownloadPDB.jl

julia> import Pkg

julia> Pkg.add("ArgParse")
   Resolving package versions...
    Updating `~/.julia/packages/MIToS/GdalX/docs/Project.toml`
  [c7e460c6] + ArgParse v1.1.4
  No Changes to `~/.julia/packages/MIToS/GdalX/docs/Manifest.toml`

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "DownloadPDB.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/DownloadPDB.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package ArgParse not found in current path:
- Run `import Pkg; Pkg.add("ArgParse")` to install the ArgParse package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/DownloadPDB.jl:6
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/DownloadPDB.jl -h`, ProcessExited(1)) [1]

Distances.jl

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Distances.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/Distances.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package MIToS not found in current path:
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/Distances.jl:6
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/Distances.jl -h`, ProcessExited(1)) [1]

MSADescription.jl

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "MSADescription.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/MSADescription.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package MIToS not found in current path:
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/MSADescription.jl:3
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/MSADescription.jl -h`, ProcessExited(1)) [1]

PercentIdentity.jl

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "PercentIdentity.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/PercentIdentity.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package MIToS not found in current path:
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/PercentIdentity.jl:8
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/PercentIdentity.jl -h`, ProcessExited(1)) [1]

AlignedColumns.jl

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "AlignedColumns.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/AlignedColumns.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package MIToS not found in current path:
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/AlignedColumns.jl:4
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/AlignedColumns.jl -h`, ProcessExited(1)) [1]

SplitStockholm.jl

julia> import Pkg

julia> Pkg.add("ArgParse")
   Resolving package versions...
  No Changes to `~/.julia/packages/MIToS/GdalX/docs/Project.toml`
  No Changes to `~/.julia/packages/MIToS/GdalX/docs/Manifest.toml`

julia> Pkg.add("CodecZlib")
   Resolving package versions...
    Updating `~/.julia/packages/MIToS/GdalX/docs/Project.toml`
  [944b1d66] + CodecZlib v0.7.0
  No Changes to `~/.julia/packages/MIToS/GdalX/docs/Manifest.toml`

julia> Pkg.add("ProgressMeter")
   Resolving package versions...
    Updating `~/.julia/packages/MIToS/GdalX/docs/Project.toml`
  [92933f4c] + ProgressMeter v1.6.2
  No Changes to `~/.julia/packages/MIToS/GdalX/docs/Manifest.toml`

julia> using MIToS

julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")
"/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia"

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "SplitStockholm.jl")
"/juliateam/.julia/packages/MIToS/GdalX/src/../scripts/SplitStockholm.jl"

julia> read(`$julia_path $script_path -h`, String) |> println
ERROR: LoadError: ArgumentError: Package ArgParse not found in current path:
- Run `import Pkg; Pkg.add("ArgParse")` to install the ArgParse package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:871
in expression starting at /juliateam/.julia/packages/MIToS/GdalX/scripts/SplitStockholm.jl:4
ERROR: failed process: Process(`/juliateam/config/sync/docfiles/julia-1.6/julia-1.6.0/bin/julia /juliateam/.julia/packages/MIToS/GdalX/src/../scripts/SplitStockholm.jl -h`, ProcessExited(1)) [1]