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Sunday, January 08, 2006

GUI version of NCBI Blastn(nr) MSH script

An NCBI Blastn (using nr database) client MSH script with winform GUI. See NCBI Blastn under MSH command line for a introduction of NCBI Blastn program.

Although personally I like command line interface, there are always some users prefer GUI. Well, since monad can use System.Windows.Forms.form, it can create comman winform GUI which is similar to what tk/tcl can do.

One of the big advantage of monad is that script block can be used a event handler.

Another thing need to mention is that monad use grave-accent(`) but not "\" for escape sequences. To get more help on escape character using command:
help about_escape_character
Because NCBI Blast server running unix like OS, so the returning results using \n but not \r\n for a new line. We have to replace those \n with \r\n to get a proper view in textbox control.



# Blastn-GUI.msh
# ===========================================================================
#
# This code is for test purposes only. Use it at your own risk.
#
# Please do not submit or retrieve more than one request every two seconds.
#
# Results will be kept at NCBI for 24 hours. For best batch performance,
# It is recommend that you submit requests after 2000 EST (0100 GMT) and
# retrieve results before 0500 EST (1000 GMT).
#
# by tony 2006 http://mshforfun.blogspot.com/
# ===========================================================================
[void] [Reflection.Assembly]::Load( `
"System.Windows.Forms, Version=2.0.0.0, Culture=neutral, `
PublicKeyToken=b77a5c561934e089")
$script:form = new-object System.Windows.Forms.form
$Panel = new-object System.Windows.Forms.Panel
$Label = new-object System.Windows.Forms.Label
$Query = new-object System.Windows.Forms.TextBox
$Submit = new-object System.Windows.Forms.Button
$script:Results = new-object System.Windows.Forms.TextBox
$script:Status = new-object System.Windows.Forms.TextBox

function SubmitQuery([String]$Sequence)
{
 if ($Sequence -match "[^ATGCatgcNn]")
 {
    $Status.Text += "Error 1: Invalid charactors in query sequence! Only A/T/G/C/N can be used!`r`n`r`n"
    $Status.Refresh()
    $Status.ScrollToCaret()
    return
 }
 
 $Status.Text += "`r`n==================================================`r`n"
 $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Submiting sequence...`r`n"
 $Status.Refresh()
 $Status.ScrollToCaret()

 $uri="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Put&PROGRAM=blastn&DATABASE=nr&QUERY=" + $Sequence
 $BlastClient = new-object System.Net.WebClient
 $pagecontent = $BlastClient.DownloadString($uri);
 if ($pagecontent -match "   RID = (.*)")
 {
   $RID=$Matches[1]
   $Status.Text += "RID =" + $RID + "`r`n"
   $Status.Refresh()
   $Status.ScrollToCaret()
  }

 if ($pagecontent -match "   RTOE = (.*)")
 {
  $TimeToComplete= $Matches[1]
  $Status.Text += "Estimated Time to finish searching: " + $TimeToComplete + " seconds`r`nWaiting...`r`n`r`n"
  $Status.Refresh()
  $Status.ScrollToCaret()
 }

 Start-sleep $TimeToComplete

 While ($true)
 {
  
   $uri= "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=" + $RID   
   $pagecontent = $BlastClient.DownloadString($uri);
   if ($pagecontent -match "Status=WAITING")
   {
    $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Search not finished yet, waiting... `r`n"
    $Status.Refresh()
    $Status.ScrollToCaret()
    Start-sleep 5
    continue
   }
   if ($pagecontent -match "Status=FAILED")
   {
     $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 2 -- Search failed!`r`n`r`n"
     $Status.Refresh()
     return
   }
   if ($pagecontent -match "Status=UNKNOWN")
   {
     $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 3-- Search expired!`r`n`r`n"
     $Status.Refresh()
     return
   }
   if ($pagecontent -match "Status=READY")
   { 
      if ($pagecontent -match "ThereAreHits=yes")
      {
         $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Search complete, retrieving results...`r`n`r`n"
     $Status.Refresh()
     $Status.ScrollToCaret()
     break
      }
      else
      {
        $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 4-- No hits found!`r`n`r`n"
    $Status.Refresh()
        return
      }
   }
   $Status.Text += (get-date).ToString("MM-dd-yyyy HH:mm") + ": Error 5-- Unknown error! `r`n`r`n"
   $Status.Refresh()
   return
}
$uri= "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=" + $RID + "&ALIGNMENTS=500&ALIGNMENT_VIEW=QueryAnchored&FORMATOBJECT=Alignment&FORMAT_TYPE=TEXT"
$Results.Text = $BlastClient.DownloadString($uri).Replace("`n","`r`n");
return
}

$form.text = "NCBI Blastn(nr) GUI"
$form.Size =  "800,600"

$Panel.Size = "794, 32"
$Panel.Location = "0, 0"

$Label.Text = "Query:"
$Label.Location = "10, 8"
$Label.Size = "80, 32"
$Panel.Controls.Add($Label)

$Query.Location = "100, 8"
$Query.Size = "500, 20"
$Panel.Controls.Add($Query)

$Submit.Location = "710, 8"
$Submit.Text = "Submit"
$Submit.Add_Click({SubmitQuery($Query.Text)})
$Panel.Controls.Add($Submit)

$form.Controls.Add($Panel)

$Results.Location = "0, 40"
$Results.Multiline = $True
$Results.Size = "790, 400"
$Results.ScrollBars = "Vertical"
$Results.ReadOnly = $true
$form.Controls.Add($Results)

$Status.Location = "0, 440"
$Status.Multiline = $True
$Status.Size = "790, 100"
$Status.ScrollBars = "Vertical"
$Status.ReadOnly = $true
$form.Controls.Add($Status)

$form.showdialog() 


[Edit: Monad has now been renamed to Windows PowerShell. This script or discussion may require slight adjustments before it applies directly to newer builds.]

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