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.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Buslje09.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/Buslje09.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

BLMI.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "BLMI.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/BLMI.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

Conservation.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Conservation.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/Conservation.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

DownloadPDB.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "DownloadPDB.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/DownloadPDB.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

Distances.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "Distances.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/Distances.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

MSADescription.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "MSADescription.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/MSADescription.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

PercentIdentity.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "PercentIdentity.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/PercentIdentity.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

AlignedColumns.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "AlignedColumns.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/AlignedColumns.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined

SplitStockholm.jl

julia> using MIToS

julia> julia_path = joinpath(Base.JULIA_HOME, "julia")
ERROR: UndefVarError: JULIA_HOME not defined

julia> script_path = joinpath(dirname(pathof(MIToS)), "..", "scripts", "SplitStockholm.jl")
"/juliateam/.julia/packages/MIToS/Hha81/src/../scripts/SplitStockholm.jl"

julia> run(`$julia_path $script_path -h`)
ERROR: UndefVarError: julia_path not defined