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")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Buslje09.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/Buslje09.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package MIToS not found in current path.
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/Buslje09.jl:7
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/Buslje09.jl -h`, ProcessExited(1)) [1]

BLMI.jl

julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "BLMI.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/BLMI.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package MIToS not found in current path.
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/BLMI.jl:7
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/BLMI.jl -h`, ProcessExited(1)) [1]

Conservation.jl

julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Conservation.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/Conservation.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package MIToS not found in current path.
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/Conservation.jl:6
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/Conservation.jl -h`, ProcessExited(1)) [1]

DownloadPDB.jl

julia> import Pkg
julia> Pkg.add("ArgParse")    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Project.toml`
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Manifest.toml`
julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "DownloadPDB.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/DownloadPDB.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package ArgParse not found in current path.
- Run `import Pkg; Pkg.add("ArgParse")` to install the ArgParse package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/DownloadPDB.jl:6
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/DownloadPDB.jl -h`, ProcessExited(1)) [1]

Distances.jl

julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Distances.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/Distances.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package MIToS not found in current path.
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/Distances.jl:6
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/Distances.jl -h`, ProcessExited(1)) [1]

MSADescription.jl

julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "MSADescription.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/MSADescription.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package MIToS not found in current path.
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/MSADescription.jl:3
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/MSADescription.jl -h`, ProcessExited(1)) [1]

PercentIdentity.jl

julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "PercentIdentity.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/PercentIdentity.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package MIToS not found in current path.
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/PercentIdentity.jl:8
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/PercentIdentity.jl -h`, ProcessExited(1)) [1]

AlignedColumns.jl

julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "AlignedColumns.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/AlignedColumns.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package MIToS not found in current path.
- Run `import Pkg; Pkg.add("MIToS")` to install the MIToS package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/AlignedColumns.jl:4
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/AlignedColumns.jl -h`, ProcessExited(1)) [1]

SplitStockholm.jl

julia> import Pkg
julia> Pkg.add("ArgParse")   Resolving package versions...
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Project.toml`
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Manifest.toml`
julia> Pkg.add("CodecZlib")   Resolving package versions...
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Project.toml`
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Manifest.toml`
julia> Pkg.add("ProgressMeter")   Resolving package versions...
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Project.toml`
  No Changes to `~/work/MIToS.jl/MIToS.jl/docs/Manifest.toml`
julia> using MIToS
julia> julia_path = joinpath(Base.Sys.BINDIR, "julia")"/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia"
julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "SplitStockholm.jl")"/home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/SplitStockholm.jl"
julia> read(`$julia_path $script_path -h`, String) |> printlnERROR: LoadError: ArgumentError: Package ArgParse not found in current path.
- Run `import Pkg; Pkg.add("ArgParse")` to install the ArgParse package.
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1766 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
in expression starting at /home/runner/work/MIToS.jl/MIToS.jl/scripts/SplitStockholm.jl:4
ERROR: failed process: Process(`/opt/hostedtoolcache/julia/1.10.0/x64/bin/julia /home/runner/work/MIToS.jl/MIToS.jl/src/../scripts/SplitStockholm.jl -h`, ProcessExited(1)) [1]