xdg-open and System.Diagnostics.Process

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As i need a program to performence the localblast from reengineering a computer model for our scientific research, so i wrote a vb.net program. when the program run into the line of start a process object to call a external command on the linux platform, the program throw me an exception:

xieguigang@xieguigang-HP-Compaq-8510w:~/Desktop/Debug$ mono ./c2.exe build -i "/home/xieguigang/Desktop/8004.gbk" -f gbk
[c2.exe, version 1.0.0.0] c2 compiler
Variable 'blastbin' = "/home/xieguigang/blast/bin/"
Variable 'blastdb' = "/home/xieguigang/blast/db/"
Export all CDS sequence from the GenBank file:
"/home/xieguigang/Desktop/8004.gbk"
Missing method .ctor in assembly /home/xieguigang/Desktop/Debug/Bio.Assembly.dll, type System.Runtime.CompilerServices.ExtensionAttribute
Can't find custom attr constructor image: /home/xieguigang/Desktop/Debug/Bio.Assembly.dll mtoken: 0x0a00003c
Data was export to file:
"/home/xieguigang/blast/db//8004.fsa"
Sequence type is proteins...
Call external command to format the target fasta database:
"/home/xieguigang/blast/bin//formatdb -i "/home/xieguigang/blast/db//8004.fsa" -p T"
xdg-open: unexpected option '-i'
Try 'xdg-open --help' for more information.
Job done!

actually the logs out put are comes from the code that shown below, its clearly that the exception is comes from the line of process.start() calling:

VB

Public Shared Sub FormatGBK(GBK As String, Optional Saved As String = "", Optional FileType As FASTATypes = FASTATypes.Protein)
    Dim Process As System.Diagnostics.Process = New System.Diagnostics.Process()

    If FileType = FASTATypes.Protein Then
          Printfn("Export all CDS sequence from the GenBank file:\n  \'%s\'", GBK)
          Dim FASTA As String = ExportAllCDS(GBK, Saved)
          Printfn("Data was export to file:\n  \'%s\'", FASTA)
          Printfn("Sequence type is proteins...")

          Process.StartInfo = Global.c2.LocalBLAST.CommandLines.FormatDb(FASTA, FileType)
          Printfn("Call external command to format the target fasta database:\n  \'%s\'", String.Format("{0} {1}", Process.StartInfo.FileName, Process.StartInfo.Arguments))
          Process.StartInfo.UseShellExecute = True
          Process.StartInfo.WindowStyle = ProcessWindowStyle.Hidden
          Call Process.Start()
          Call Process.WaitForExit()
          Printfn("Job done!")
     ElseIf FileType = FASTATypes.Nucleotide Then

the System.Diagnostics.Process object in the statement is not working.....

I know the xdg-open is an application on the linux platform which have the same function as the object ' System.Diagnostics.Process' in vb.net

so how to deal with this situation on the linux platform when i using the vb.net program to call an external command?

Posted 15-Oct-13 18:25pm

Mr. xieguigang 谢桂纲

Updated 15-Oct-13 19:20pm

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Sergey Alexandrovich Kryukov 16-Oct-13 0:27am

Are you using Mono?
—SA

Mr. xieguigang 谢桂纲 16-Oct-13 1:02am

yes, mono 2.1 on Ubnuntu 13.04

Sergey Alexandrovich Kryukov 16-Oct-13 2:21am

Very good, thank you for answering.
—SA

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Sergey Alexandrovich Kryukov · Answer 1 · 2013-10-15T18:34:00

This code should not even compile. The instance of Process.StartInfo should first be created; Process.Start accepts one or two arguments (if you use , and the method Process.ForExit is not static, should be called with the process instance obtained from previous call.
And so on… I don't even know what to advise. Well… learn the very basic of programming, .NET programming and some of .NET BCL and FCL. At least read original MDSN documentation before writing code:
http://msdn.microsoft.com/en-us/library/system.diagnostics.process.aspx[^].

However, I am not sure it can help you, because I am not sure you have any idea of classes, other types and their instances (objects), instance vs. static members and a lot more. Most likely, you need to learn all that.

—SA