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WM.frm
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WM.frm
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VERSION 5.00
Begin VB.Form Form1
Caption = "Demo - motif detection"
ClientHeight = 11265
ClientLeft = 5880
ClientTop = 1950
ClientWidth = 17580
LinkTopic = "Form1"
Picture = "WM.frx":0000
ScaleHeight = 751
ScaleMode = 3 'Pixel
ScaleWidth = 1172
StartUpPosition = 2 'CenterScreen
Begin VB.CheckBox y_axis
Caption = "Reverse axis"
Height = 350
Left = 9840
TabIndex = 46
Top = 0
Width = 1215
End
Begin VB.Frame MatrixXYZ
Caption = "General information"
Height = 5055
Left = 4920
TabIndex = 9
Top = 5280
Width = 7215
Begin VB.CommandButton ShowVariants
Caption = "Text matrix"
Height = 375
Index = 0
Left = 240
TabIndex = 27
Top = 360
Width = 1335
End
Begin VB.CommandButton ShowVariants
Caption = "Count matrix"
Height = 375
Index = 1
Left = 1560
TabIndex = 26
ToolTipText = "Position Frequency Matrix (PFM)"
Top = 360
Width = 1335
End
Begin VB.CommandButton ShowVariants
Caption = "Weight matrix"
Height = 375
Index = 2
Left = 2880
TabIndex = 25
ToolTipText = "Position Probability Matrix (PPM)"
Top = 360
Width = 1335
End
Begin VB.CommandButton ShowVariants
Caption = "LogRatio matrix"
Height = 375
Index = 3
Left = 4200
TabIndex = 24
ToolTipText = " Position Weight Matrix (PWM)"
Top = 360
Width = 1575
End
Begin VB.CommandButton ShowVariants
Caption = "Info"
BeginProperty Font
Name = "MS Sans Serif"
Size = 8.25
Charset = 0
Weight = 700
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 375
Index = 4
Left = 5760
TabIndex = 23
Top = 360
Width = 1215
End
Begin VB.PictureBox IF_holder
Appearance = 0 'Flat
AutoRedraw = -1 'True
ForeColor = &H80000008&
Height = 4215
Left = 240
ScaleHeight = 279
ScaleMode = 3 'Pixel
ScaleWidth = 447
TabIndex = 22
Top = 720
Width = 6735
Begin VB.PictureBox NPSet
Appearance = 0 'Flat
AutoRedraw = -1 'True
BackColor = &H80000005&
ForeColor = &H80000008&
Height = 1575
Left = 5040
Picture = "WM.frx":0446
ScaleHeight = 103
ScaleMode = 3 'Pixel
ScaleWidth = 95
TabIndex = 42
Top = 120
Visible = 0 'False
Width = 1455
End
Begin VB.PictureBox FreqPanel
Appearance = 0 'Flat
AutoRedraw = -1 'True
BackColor = &H80000005&
ForeColor = &H80000008&
Height = 2175
Left = 240
ScaleHeight = 143
ScaleMode = 3 'Pixel
ScaleWidth = 415
TabIndex = 34
Top = 1800
Width = 6255
End
Begin VB.Line Line2
BorderColor = &H00C0C0C0&
X1 = 16
X2 = 416
Y1 = 64
Y2 = 64
End
Begin VB.Label w_pos
BackStyle = 0 'Transparent
Caption = "..."
BeginProperty Font
Name = "Lucida Console"
Size = 12
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
ForeColor = &H00808080&
Height = 375
Left = 240
TabIndex = 43
Top = 600
Width = 6255
End
Begin VB.Label Label3
BackStyle = 0 'Transparent
Caption = "Unordered Sequence Logo:"
BeginProperty Font
Name = "Lucida Console"
Size = 12
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
ForeColor = &H00808080&
Height = 375
Left = 240
TabIndex = 36
Top = 1440
Width = 6255
End
End
Begin VB.PictureBox MP_holder
AutoRedraw = -1 'True
BackColor = &H00FFFFFF&
Height = 4215
Left = 240
ScaleHeight = 277
ScaleMode = 3 'Pixel
ScaleWidth = 445
TabIndex = 20
Top = 720
Visible = 0 'False
Width = 6735
Begin VB.CheckBox Fallow_M
BackColor = &H00FFFFFF&
Caption = "Fallow Matrix !"
Height = 375
Left = 600
TabIndex = 32
Top = 3120
Value = 1 'Checked
Width = 1935
End
Begin VB.TextBox Mlog
Appearance = 0 'Flat
BackColor = &H00C0FFC0&
Height = 285
Index = 0
Left = 5760
TabIndex = 21
Text = "0"
Top = 120
Visible = 0 'False
Width = 495
End
End
Begin VB.PictureBox MW_holder
AutoRedraw = -1 'True
BackColor = &H00FFFFFF&
Height = 4215
Left = 240
ScaleHeight = 277
ScaleMode = 3 'Pixel
ScaleWidth = 445
TabIndex = 18
Top = 720
Visible = 0 'False
Width = 6735
Begin VB.CheckBox FollowWM
BackColor = &H00FFFFFF&
Caption = "Follow Weight Matrix"
Height = 255
Left = 480
TabIndex = 33
Top = 3120
Value = 1 'Checked
Width = 2055
End
Begin VB.TextBox Mwght
Appearance = 0 'Flat
BackColor = &H00C0FFFF&
Height = 285
Index = 0
Left = 5760
TabIndex = 19
Text = "0"
Top = 120
Visible = 0 'False
Width = 495
End
End
Begin VB.PictureBox MV_holder
AutoRedraw = -1 'True
BackColor = &H00FFFFFF&
Height = 4215
Left = 240
ScaleHeight = 277
ScaleMode = 3 'Pixel
ScaleWidth = 445
TabIndex = 16
Top = 720
Visible = 0 'False
Width = 6735
Begin VB.TextBox Mval
Appearance = 0 'Flat
BackColor = &H00C0E0FF&
Height = 285
Index = 0
Left = 5760
TabIndex = 17
Text = "0"
Top = 120
Visible = 0 'False
Width = 495
End
End
Begin VB.PictureBox MT_holder
AutoRedraw = -1 'True
BackColor = &H00FFFFFF&
Height = 4215
Left = 240
ScaleHeight = 277
ScaleMode = 3 'Pixel
ScaleWidth = 445
TabIndex = 14
Top = 720
Visible = 0 'False
Width = 6735
Begin VB.TextBox MTxt
Appearance = 0 'Flat
BackColor = &H00C0C0FF&
Height = 285
Index = 0
Left = 5760
TabIndex = 15
Text = "0"
Top = 120
Visible = 0 'False
Width = 495
End
End
End
Begin VB.Frame Frame2
Caption = "Parameters"
Height = 5055
Left = 12360
TabIndex = 6
Top = 5280
Width = 5055
Begin VB.Frame Frame5
Caption = "Make score values from:"
Height = 2415
Left = 240
TabIndex = 28
Top = 2400
Width = 4575
Begin VB.CheckBox LR_DANU
Caption = "Use the values from Position Weight Matrix (PWM)"
Height = 375
Index = 0
Left = 240
TabIndex = 31
ToolTipText = "sum from the LogRatio matrix ..."
Top = 480
Value = 1 'Checked
Width = 4215
End
Begin VB.CommandButton Scann
Caption = "Scan for motif"
BeginProperty Font
Name = "MS Sans Serif"
Size = 8.25
Charset = 0
Weight = 700
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 615
Left = 240
TabIndex = 30
Top = 1560
Width = 4095
End
Begin VB.CheckBox LR_DANU
Caption = "Use the values from Position Probability Matrix (PPM)"
Height = 375
Index = 1
Left = 240
TabIndex = 29
ToolTipText = "sum from the Weight matrix ..."
Top = 960
Width = 4215
End
End
Begin VB.Frame Frame3
Caption = "Zoom on signal"
Height = 1455
Left = 240
TabIndex = 10
Top = 720
Width = 4575
Begin VB.OptionButton ZSO
Caption = "Zoom signal"
Height = 255
Left = 240
TabIndex = 13
Top = 360
Value = -1 'True
Width = 1215
End
Begin VB.OptionButton SLO
Caption = "Signal level (with follow matrix option)"
Height = 255
Left = 240
TabIndex = 12
Top = 840
Width = 3975
End
Begin VB.HScrollBar Zoom_Scale
Height = 255
Left = 1560
Max = 200
Min = 4
TabIndex = 11
Top = 360
Value = 30
Width = 2895
End
End
Begin VB.Timer RealTime
Interval = 100
Left = 4440
Top = 240
End
Begin VB.TextBox Lungime_fereastra
Enabled = 0 'False
Height = 285
Left = 3000
TabIndex = 7
Text = "30"
Top = 360
Width = 615
End
Begin VB.Label Label2
Alignment = 1 'Right Justify
BackStyle = 0 'Transparent
Caption = "Sliding window length:"
Height = 255
Left = 960
TabIndex = 8
Top = 360
Width = 1935
End
End
Begin VB.Frame Frame1
Caption = "The motif set (input)"
Height = 5055
Left = 240
TabIndex = 3
Top = 5280
Width = 4455
Begin VB.OptionButton Val_Z
Caption = "Initialize PFM with zero values"
Height = 255
Left = 240
TabIndex = 45
ToolTipText = "Position Frequency Matrix (PFM), also known as the count matrix"
Top = 3840
Value = -1 'True
Width = 3975
End
Begin VB.OptionButton Val_P
Caption = "Initialize PFM with pseudocounts (0.000001)"
Height = 255
Left = 240
TabIndex = 44
ToolTipText = "Position Frequency Matrix (PFM), also known as the count matrix"
Top = 3480
Width = 3975
End
Begin VB.TextBox WMatrix
BeginProperty Font
Name = "Courier New"
Size = 12
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 2895
Left = 240
MultiLine = -1 'True
ScrollBars = 2 'Vertical
TabIndex = 5
Text = "WM.frx":2C78
Top = 360
Width = 3975
End
Begin VB.CommandButton Make_Matrix
Caption = "Make Position weight matrix (PWM)"
Height = 615
Left = 240
TabIndex = 4
Top = 4200
Width = 3975
End
End
Begin VB.PictureBox Center_patt
AutoRedraw = -1 'True
BackColor = &H00FFFFFF&
Height = 4695
Left = 12360
ScaleHeight = 309
ScaleMode = 3 'Pixel
ScaleWidth = 333
TabIndex = 2
Top = 360
Width = 5055
Begin VB.Line Line10
BorderStyle = 3 'Dot
X1 = 168
X2 = 168
Y1 = 0
Y2 = 312
End
Begin VB.Line Line9
BorderStyle = 3 'Dot
X1 = 336
X2 = -8
Y1 = 152
Y2 = 152
End
End
Begin VB.PictureBox Picture1
AutoRedraw = -1 'True
BackColor = &H00FFFFFF&
Height = 2415
Left = 240
ScaleHeight = 157
ScaleMode = 3 'Pixel
ScaleWidth = 717
TabIndex = 1
Top = 360
Width = 10815
Begin VB.Label down_label
BackStyle = 0 'Transparent
Caption = "Different from the motif set (red)"
BeginProperty Font
Name = "Lucida Console"
Size = 8.25
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 255
Left = 120
TabIndex = 39
Top = 2040
Width = 5175
End
Begin VB.Label up_label
BackStyle = 0 'Transparent
Caption = "Like the motif set (blue)"
BeginProperty Font
Name = "Lucida Console"
Size = 8.25
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 255
Left = 120
TabIndex = 38
Top = 120
Width = 4455
End
Begin VB.Line Zero
BorderColor = &H00404040&
X1 = 0
X2 = 728
Y1 = 80
Y2 = 80
End
Begin VB.Shape Window_Shape
BorderColor = &H00808080&
Height = 4095
Left = 0
Top = 0
Visible = 0 'False
Width = 15
End
End
Begin VB.TextBox secventata
Height = 2055
Left = 240
MultiLine = -1 'True
ScrollBars = 2 'Vertical
TabIndex = 0
Text = "WM.frx":2CE7
Top = 3120
Width = 11895
End
Begin VB.Line Line6
X1 = 744
X2 = 744
Y1 = 176
Y2 = 192
End
Begin VB.Line Line5
X1 = 744
X2 = 744
Y1 = 16
Y2 = 32
End
Begin VB.Line Line4
X1 = 744
X2 = 720
Y1 = 24
Y2 = 24
End
Begin VB.Line Line3
X1 = 744
X2 = 720
Y1 = 184
Y2 = 184
End
Begin VB.Label down_val
BackStyle = 0 'Transparent
Caption = "0"
BeginProperty Font
Name = "Lucida Console"
Size = 11.25
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 255
Left = 11280
TabIndex = 48
Top = 2640
Width = 855
End
Begin VB.Label up_val
BackStyle = 0 'Transparent
Caption = "0"
BeginProperty Font
Name = "Lucida Console"
Size = 11.25
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 255
Left = 11280
TabIndex = 47
Top = 240
Width = 855
End
Begin VB.Image Image1
Height = 720
Left = -7680
Picture = "WM.frx":343C
Top = 10560
Width = 25290
End
Begin VB.Label Label8
BackStyle = 0 'Transparent
Caption = "Zoom into the signal using the sliding window length:"
Height = 255
Left = 12360
TabIndex = 41
Top = 120
Width = 4815
End
Begin VB.Label Label7
BackStyle = 0 'Transparent
Caption = "The main signal over the entire sequence:"
Height = 255
Left = 240
TabIndex = 40
Top = 120
Width = 5415
End
Begin VB.Label Label4
Caption = "0"
BeginProperty Font
Name = "Lucida Console"
Size = 11.25
Charset = 0
Weight = 400
Underline = 0 'False
Italic = 0 'False
Strikethrough = 0 'False
EndProperty
Height = 255
Left = 11280
TabIndex = 37
Top = 1440
Width = 135
End
Begin VB.Line Line1
X1 = 728
X2 = 744
Y1 = 104
Y2 = 104
End
Begin VB.Label Label1
BackStyle = 0 'Transparent
Caption = "Find motif in sequence:"
Height = 255
Left = 240
TabIndex = 35
Top = 2880
Width = 4935
End
End
Attribute VB_Name = "Form1"
Attribute VB_GlobalNameSpace = False
Attribute VB_Creatable = False
Attribute VB_PredeclaredId = True
Attribute VB_Exposed = False
' ________________________________ ____________________
' / Demo - motif detection \________________________/ v1.00 |
' | |
' | Name: Demo - motif detection V1.0 |
' | Category: Open source software |
' | Author: Paul A. Gagniuc |
' | Book: Algorithms in Bioinformatics: Theory and Implementation |
' | Email: [email protected] |
' | ____________________________________________________________________________ |
' | |
' | Date Created: January 2014 |
' | Update: August 2021 |
' | Tested On: WinXP, WinVista, Win7, Win8, Win10 |
' | Use: Analysis of splice sites |
' | |
' | _____________________________ |
' |_________________/ \_______________________________|
'
Dim M() As String 'stores the rows for Matrix ()
Dim Weight() As String 'proportions
Dim Matrix() As String 'matrix of nucleotides
Dim Matrix_Val() As String 'no of A and T and C and G in cols of Matrix()
Dim Weight_Max() As String 'order by max values
Dim MLogRatio() As String 'Log weight
'######################
Dim MX_pos As Variant
Dim MY_pos As Variant
Dim space_x As Integer
Dim space_y As Integer
'######################
Dim Interface_on As Boolean
Dim select_start_reminder As Integer
Private Sub Form_Load()
Interface_on = False
'##################
MX_pos = 20
MY_pos = 25
space_x = 3
space_y = 3
'##################
secventata.Text = Replace(secventata.Text, Chr(10), "")
secventata.Text = Replace(secventata.Text, Chr(13), "")
'X
Line9.X1 = 0
Line9.X2 = Center_patt.ScaleWidth
Line9.Y1 = (Center_patt.ScaleHeight / 2)
Line9.Y2 = (Center_patt.ScaleHeight / 2)
Line9.Visible = True
'Y
Line10.X1 = (Center_patt.ScaleWidth / 2)
Line10.X2 = (Center_patt.ScaleWidth / 2)
Line10.Y1 = 0
Line10.Y2 = Center_patt.ScaleWidth
Line10.Visible = True
Line1.Y1 = Picture1.Top + (Picture1.ScaleHeight / 2) + 2
Line1.Y2 = Line1.Y1
Zero.Y1 = (Picture1.ScaleHeight / 2)
Zero.Y2 = Zero.Y1
Label4.Top = Line1.Y1 - (Label4.Height / 2) + 3
'Make_Matrix_Click
DoEvents
Scann_Click
End Sub
Private Sub LR_DANU_MouseUp(Index As Integer, Button As Integer, Shift As Integer, X As Single, Y As Single)
For i = 0 To LR_DANU.UBound
LR_DANU(i).Value = 0
Next i
LR_DANU(Index).Value = 1
Scann_Click
DoEvents
ShowVariants_Click (4)
End Sub
'##########################################################################
'##########################################################################
'##########################################################################
Private Sub Make_Matrix_Click()
'Format textbox in case of bad input
'--------------------------------------------------------------------------
If Len(WMatrix.Text) < 3 Then Exit Sub
WMatrix.Text = UCase(WMatrix.Text)
WMatrix.Text = Replace(WMatrix.Text, vbCrLf & vbCrLf, vbCrLf)
Dim ttmp() As String
ttmp() = Split(WMatrix.Text, vbCrLf)
If (ttmp(UBound(ttmp())) > "") Then WMatrix.Text = WMatrix.Text & vbCrLf
s = WMatrix.Text
t = (Len(s) - Len(Replace(s, vbCrLf, ""))) / 2 '[vbcrlf represents two chr]
Frame1.Caption = "The motif set (input): " & t & " motifs"
'--------------------------------------------------------------------------
M() = Split(WMatrix.Text, vbCrLf)
Rows = UBound(M()) - 1
cols = Len(M(0)) - 1
'------ Matrix(n,n) umplut cu caractere -----------------------------------
ReDim Matrix(0 To Rows, 0 To cols) As String
For i = 0 To Rows
For j = 0 To cols
Matrix(i, j) = Mid(M(i), j + 1, 1)
'MsgBox "Matrix(" & i & "|" & j & ")" & Mid(M(i), j + 1, 1)
Next j
Next i
'--------------------------------------------------------------------------
'------ Matrix_Val(n,4) umplut cu valori ----------------------------------
Dim Xb(0 To 3) As String
ReDim Matrix_Val(0 To 3, 0 To cols) As String
For j = 0 To cols
For e = 0 To 3
If Val_Z.Value = True Then Xb(e) = 0
If Val_P.Value = True Then Xb(e) = 0.000001
Next e
For i = 0 To Rows
n = Matrix(i, j)
If n = "A" Then Xb(0) = Xb(0) + 1
If n = "C" Then Xb(1) = Xb(1) + 1
If n = "G" Then Xb(2) = Xb(2) + 1
If n = "T" Then Xb(3) = Xb(3) + 1
Next i
For v = 0 To 3
Matrix_Val(v, j) = Xb(v)
'MsgBox "col = " & j & vbCrLf & "v= " & Xb(v)
Next v
Next j
'--------------------------------------------------------------------------
'------ Weight Matrix (0 to 1 values for each nucleotide in the row) ------
ReDim Weight(0 To cols, 0 To 3) As String
Dim nx(0 To 3) As String
For j = 0 To cols
For v = 0 To 3
nx(v) = Val(Matrix_Val(v, j))
Next v
For v = 0 To 3
'Weight(j, v) = (1 / (Val(nx(0)) + Val(nx(1)) + Val(nx(2)) + Val(nx(3)))) * Val(Matrix_Val(v, j))
If Val_Z.Value = True Then Weight(j, v) = Round(Val(Matrix_Val(v, j)) / (Rows + 1), 1)
If Val_P.Value = True Then Weight(j, v) = Val(Matrix_Val(v, j)) / (Rows + 1)
'----------------------
'If v = 0 Then X = "A"
'If v = 1 Then X = "C"
'If v = 2 Then X = "G"
'If v = 3 Then X = "T"
'MsgBox "col = " & j & vbCrLf & "v= " & X & vbCrLf & Matrix_Val(v, j) & vbCrLf & Weight(j, v)
'---------------------
Next v
Next j
'--------------------------------------------------------------------------
'------ MLogRatio (Log ratio = N/0.25) ------------------------------------
ReDim MLogRatio(0 To cols, 0 To 3) As String
Dim nl(0 To 3) As String
For j = 0 To cols
For v = 0 To 3
If Val(Weight(j, v)) = 0 Then
MLogRatio(j, v) = 0
Else
MLogRatio(j, v) = Round(Log(Val(Weight(j, v)) / 0.25), 3)
End If
'----------------------
'If v = 0 Then X = "A"
'If v = 1 Then X = "C"
'If v = 2 Then X = "G"
'If v = 3 Then X = "T"
'MsgBox "col = " & j & vbCrLf & "v= " & X & vbCrLf & vbCrLf & MLogRatio(j, v)
'---------------------
Next v
Next j
'--------------------------------------------------------------------------
Call FreqNuc(Len(M(0)))
ShowVariants_Click (4)
End Sub
Function FreqNuc(ByVal cols As Integer)
Dim aY(0 To 3) As Integer
xBuc = FreqPanel.ScaleWidth / cols
ybuc = FreqPanel.ScaleHeight / 100
For i = 1 To cols
plus = 0
For j = 0 To 3
If j = 0 Then
sX = 0
sY = 0
sW = 46
sH = 47
xColor = vbGreen 'A
End If
If j = 1 Then
sX = 46
sY = 0
sW = 41
sH = 47
xColor = vbRed 'C
End If
If j = 2 Then
sX = 43
sY = 49
sW = 44
sH = 49
xColor = vbBlue 'G
End If
If j = 3 Then
sX = 4
sY = 50
sW = 38
sH = 47
xColor = vbYellow 'T
End If
aY(j) = Val(Weight(i - 1, j)) * 100 'Nx4 (Weight(0 To Cols, 0 To 3))
'FreqPanel.Line (xBuc * oldi, plus)-(xBuc * i, plus + (ybuc * aY(j))), xColor, BF
pX = xBuc * oldi
pY = plus
pWith = xBuc
pHeight = (ybuc * aY(j)) + 1
FreqPanel.PaintPicture NPSet.Picture, pX, pY, pWith, pHeight, sX, sY, sW, sH, vbSrcCopy
plus = plus + (ybuc * aY(j))
'Debug.Print aY(j)
Next j
oldi = i
Next i
End Function
'Public Function SortArray(ByRef TheArray As Variant)
'Sorted = False
'Do While Not Sorted
' Sorted = True
'For X = 0 To UBound(TheArray) - 1
' If TheArray(X) > TheArray(X + 1) Then
' Temp = TheArray(X + 1)
' TheArray(X + 1) = TheArray(X)
' TheArray(X) = Temp