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App.xojo_code
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App.xojo_code
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#tag Class
Protected Class App
Inherits Application
#tag Event
Sub Activate()
End Sub
#tag EndEvent
#tag Event
Sub EnableMenuItems()
FileMakeSigFile.visible=false
FileConvertSigFilestoFolders.visible=false
if Keyboard.AltKey then
FileMakeSigFile.Visible=true
FileMakeSigFile.Enabled=true
FileConvertSigFilestoFolders.visible=True
FileConvertSigFilestoFolders.Enabled=True
end if
'Build dynamic Window Menu
dim count, i as Integer
// Get a handle to our parent sub menu.
Dim parent, child as MenuItem
parent = MainMenuBar.Child( kWindows ) // Get the window menu
if parent = nil then return
// Clear the existing menu
for i=parent.Count-1 downto 0
parent.Remove(i)
next
// Add the windows to the menu
count = WindowCount
for i = 0 to count - 1
// Construct the child item
if Window(i).visible then
child = new WindowMenuItem(Window(i))
if i=0 then
'add checkmark to the front window menuitem
child.Checked=true
end if
// And add it to the menu
parent.Append( child )
end if
next i
if Window(0) isA GenomeWin or Window(0) isA RegPreciseWin or Window(0) isA WebBrowserWin or Window(0) isA HelpWin then
FileClose.enabled=true
end if
RegulonGetRegPreciseTFseqs.visible=false
'hide debug/development menus for builds
#if DebugBuild
GenomeGetCRtags.visible=true
GenomeCRtagfilteredsearch.visible=true
GenomeRunMEMEtwice.visible=true
GenomeRedundantSeqs.visible=true
LogoFromPWMtest.visible=true
#else
GenomeGetCRtags.visible=false
GenomeCRtagfilteredsearch.visible=false
GenomeRunMEMEtwice.visible=false
GenomeRedundantSeqs.visible=false
LogoFromPWMtest.visible=false
#endif
End Sub
#tag EndEvent
#tag Event
Sub Open()
SetLinuxIcon
DisableAppAutoTabbing
GetResources_f
ReadPrefs 'diplicating this function in several places as event order is different on different systems
'initialise array for reverse-complementation (and complementation):
'A-65 -> T-84
'B-66 -> V-86
'C-67 -> G-71
'D-68 -> H-72
'G-71 -> C-67
'H-72 -> D-68
'K-75 -> M-77
'M-77 -> K-75
'N-78 -> N-78
'R-82 -> Y-89
'S-83 -> S-83
'T-84 -> A-65
'V-86 -> B-66
'W-87 -> W-87
'X-88 -> X-88
'Y-89 -> R-82
dim RCCodes as string="84,86,71,72,69,70,67,68,73,74,77,76,75,78,79,80,81,89,83,65,85,66,87,88,82"
'first simply fill the array with the default values
'so that non-DNA characters are preserved:
dim n as integer
for n=0 to 256
RevCompArr(n)=n
next
'now go upper case letters:
for n=0 to 24
RevCompArr(n+65)=val(midB(RCCodes,(3*n+1),2))
next
'lower case values are higher by 32:
for n=0 to 24
RevCompArr(n+97)=val(midB(RCCodes,(3*n+1),2))+32
next
GeneticCodesInit
ProfileWizardWin.hide 'initialise to avoid showing at profile calibration
#if targetwin32 then
'No luck with this on Windows, use the 'Convert to MEME' command
'(does the same, but outputs plain text to the log pane)
AlignmentMEME.Enabled=false
AlignmentMEME.Visible=false
#endif
End Sub
#tag EndEvent
#tag Event
Sub OpenDocument(item As FolderItem)
If item<> Nil Then
select case item.Type
case "GenBank"
if GenomeWin.SaveCheck then
GenomeWin.opengenbankfile(item)
GenomeWin.ShowGenomeStart
LogoWin.GenomeFile=item
end if
case "Fasta"
logowin.LoadAlignment(item)
if LengthsDiffer then
logowin.ChangeView("Sequences")
LogoWin.LogoTabs.TabIndex=1
else
logowin.ChangeView("Logo")
LogoWin.LogoTabs.TabIndex=0
end if
logowin.title="SigmoID: "+item.DisplayName
case "SigmoidFile"
logowin.LoadAlignment(item)
logowin.ChangeView("Logo")
logowin.LogoTabs.TabIndex=0
logowin.title="SigmoID: "+item.DisplayName
end select
end if
End Sub
#tag EndEvent
#tag MenuHandler
Function AboutSigmoID() As Boolean Handles AboutSigmoID.Action
About.Show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function ChipMdata2Logo() As Boolean Handles ChipMdata2Logo.Action
ChipMdata2Logo
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function CRtagbase(index as Integer) As Boolean Handles CRtagbase.Action
CRtagBaseConstructor.Show
return true
End Function
#tag EndMenuHandler
#tag MenuHandler
Function EditPreferences() As Boolean Handles EditPreferences.Action
SettingsWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function FileConvertSigFilestoFolders() As Boolean Handles FileConvertSigFilestoFolders.Action
// Convert all .sig files in the current profiles folder into folders with the same names
// required to overcome the 64-bit compiler bug
Dim OutF, SigF, f As FolderItem
Dim m,n,p,q as integer
dim basename as string
dim vv as VirtualVolume
Dim dlg As New SelectFolderDialog
dlg.ActionButtonCaption = "Select"
dlg.Title = "Select Folder for Converted Profiles"
dlg.PromptText = "Select a Folder to store converted .sig files"
dlg.InitialDirectory = Profile_f.parent
OutF = dlg.ShowModal
If OutF <> Nil Then
'Profile_f is currently used
m=Profile_f.Count
for n=1 to m
if Profile_f.Item(n).name<>".DS_Store" then
if Profile_f.Item(n).Directory then
'skip folder
else
if right(Profile_f.Item(n).Name,4)=".sig" then
'create the folder:
SigF=OutF.child(Profile_f.Item(n).Name)
SigF.createAsFolder
if not SigF.Exists or not SigF.Directory Then
// folder was not created - abort
Return False
End If
'copy files:
vv=Profile_f.Item(n).openAsVirtualVolume
if vv<> nil then
basename=nthfield(Profile_f.Item(n).DisplayName,".sig",1)
f=vv.root.child(basename+".fasta")
if f<> NIL and f.exists then
f.CopyFileTo SigF
end if
f=vv.root.child(basename+".hmm")
if f<> NIL and f.exists then
f.CopyFileTo SigF
end if
f=vv.root.child(basename+".info")
if f<> NIL and f.exists then
f.CopyFileTo SigF
end if
f=vv.root.child(basename+".options")
if f<> NIL and f.exists then
f.CopyFileTo SigF
end if
f=vv.root.child("meme.txt")
if f<> NIL and f.exists then
f.CopyFileTo SigF
end if
else
beep
end if
end if
end if
end if
next
logowin.WriteToSTDOUT(EndOfLine+"Converted sig files written to "+OutF.ShellPath+EndOfLine)
Else
// User cancelled
End If
Exception err
ExceptionHandler(err,"App:FileConvertSigFilestoFolders")
End Function
#tag EndMenuHandler
#tag MenuHandler
Function FileListAllRegulonDBdata() As Boolean Handles FileListAllRegulonDBdata.Action
RegulonDBwin.RegulonDBfile=Resources_f.child("RegulonDB").child("BindingSiteSet.txt")
if RegulonDBWin.RegulonDBfile<>Nil and RegulonDBWin.RegulonDBfile.Exists then
RegulonDBWin.show
RegulonDBWin.FillRegulatorList(RegulonDBWin.RegulonDBfile)
else
LogoWin.WriteToSTDOUT("RegulonDB data file is missing")
end if
End Function
#tag EndMenuHandler
#tag MenuHandler
Function FileMakeSigFile() As Boolean Handles FileMakeSigFile.Action
Dim dlg As New SelectFolderDialog
dlg.ActionButtonCaption = "Make .sig"
dlg.Title = "Convert Folder to .sig File "
dlg.PromptText = "Select folder with .fasta, .options and .info files to convert"
dlg.InitialDirectory = Profile_f
Dim f As FolderItem
f = dlg.ShowModal
If f <> Nil Then
MakeSigFile f
Else
// User cancelled
End If
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function FileOpen() As Boolean Handles FileOpen.Action
'open genbank file in genome browser and display 9 kb of it
if GenomeWin.SaveCheck then 'save changes in the open file if any
dim GenomeFile as folderitem
Dim dlg As New OpenDialog
'#If Not TargetLinux Then
'dlg.InitialDirectory = SpecialFolder.Documents
'#Else //open Home directory on linux
'dlg.InitialDirectory = SpecialFolder.Home
'#Endif
'dlg.promptText="Select a GenBank file"
dlg.Title="Open GenBank file"
dlg.Filter=FileTypes.GenBank
GenomeFile=dlg.ShowModal()
if GenomeFile<> Nil then
GenomeWin.opengenbankfile(GenomeFile)
LogoWin.GenomeFile=GenomeFile
FastaButtonsCheck
GenomeWin.ShowGenomeStart
end if
Return True
end if
End Function
#tag EndMenuHandler
#tag MenuHandler
Function FileOpenAlignment() As Boolean Handles FileOpenAlignment.Action
dim tmpfile as folderitem
'#Else
Dim dlg as New OpenDialog
dlg.promptText="Select an alignment file"
dlg.Title="Open alignment"
#If XojoVersion < 2017.02
#if Target64Bit
'64 bit compiler has VirtualVolumes badly broken, hence we just can't open .sig files
'and they are converted to folders that could be only opened from the toolbar
dlg.Filter=FileTypes.Fasta' + FileTypes.Sig_file
#else
dlg.Filter=FileTypes.Fasta + FileTypes.Sig_file
#endif
#else
dlg.Filter=FileTypes.Fasta + FileTypes.Sig_file
#endif
tmpfile=dlg.ShowModal 'within(self)
'#endif
if tmpfile<>nil then
logowin.Title="SigmoID: "+NthField(tmpfile.name,".",1)
logowin.LoadAlignment(tmpFile)
logowin.ChangeView("Logo")
logowin.LogoTabs.TabIndex=0
Return True
end if
End Function
#tag EndMenuHandler
#tag MenuHandler
Function FileOpenRegulonDBdata() As Boolean Handles FileOpenRegulonDBdata.Action
dim tmpfile, convertedFasta as folderitem
dim GenomeFile as folderitem
Dim dlg As New OpenDialog
dlg.promptText="Select a file with RegulonDB data for a SINGLE regulator"
'dlg.SuggestedFileName=nthfield(GenomeFile.Name,".",1)+".tbl"
dlg.Title="Open RegulonDB data"
'dlg.Filter=FileTypes.Fasta + FileTypes.Sig_file
tmpfile=dlg.ShowModal 'within(self)
if tmpfile<>nil then
convertedFasta=TemporaryFolder.child("converted.fasta")
if convertedFasta<>nil then
RegulonDB2fasta(tmpfile,convertedFasta)
logowin.Title="SigmoID: "+NthField(tmpfile.name,".",1)
logowin.LoadAlignment(convertedFasta)
logowin.ChangeView("Logo")
logowin.LogoTabs.TabIndex=0
end if
Return True
end if
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function FilterDuplicateSites() As Boolean Handles FilterDuplicateSites.Action
LogoWin.filerRedundancy
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function GenomeCRtagfilteredsearch() As Boolean Handles GenomeCRtagfilteredsearch.Action
FilteredSearchWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function GenomeDeNovoTFBSinference() As Boolean Handles GenomeDeNovoTFBSinference.Action
deNovoWin.show
End Function
#tag EndMenuHandler
#tag MenuHandler
Function GenomeGetCRtags() As Boolean Handles GenomeGetCRtags.Action
CRtagWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function GenomeRedundantSeqs() As Boolean Handles GenomeRedundantSeqs.Action
RedundantSeqWin.show
End Function
#tag EndMenuHandler
#tag MenuHandler
Function GenomeRunMEMEtwice() As Boolean Handles GenomeRunMEMEtwice.Action
// Runs MEME twice (in zoops and anr modes), each time looking for five motifs.
' Results are stored in two subfolders within selected location.
Dim MEMEf As FolderItem
Dim OutF as folderitem
Dim dlg As New SelectFolderDialog
dlg.ActionButtonCaption = "Select"
dlg.Title = "Select Folder for MEME Output"
dlg.PromptText = "Select a folder to store MEME results"
'dlg.InitialDirectory = Profile_f.parent
OutF = dlg.ShowModal
If OutF <> Nil Then
dim opt as string
dim ErrCode as integer
'copy alignment out of virtual volume:
dim alignment_tmp as folderitem = TemporaryFolder.child("alignment.tmp")
if alignment_tmp<>NIL then
if alignment_tmp.Exists then
alignment_tmp.Delete
end if
LogoWin.LogoFile.CopyFileTo alignment_tmp
else
msgbox "Can't create temporary file!"
'return -1
end if
if CPUcores>1 then
opt=" -p " + str(CPUcores) 'for parallelised meme
end if
opt=opt+" -dna -minw 17"+" -maxw 23"
'[-pal] force palindromes (requires -dna)
'if PalindromicBox.Value then
opt=opt+" -pal"
'end if
'[-revcomp] allow sites on + or - DNA strands
'if GivenStrandBox.Value then
'else
opt=opt+" -revcomp"
'end if
'[-nmotifs <nmotifs>] maximum number of motifs to find
opt=opt+" -nmotifs 5"'+MotifNoPopup.Text
'Run MEME in Zero or One per sequence' mode:
MEMEf=OutF.child("Zoops")
FixPath4Windows(MEMEf)
if MEMEf<>NIL then
if MEMEf.Exists then
MEMEf.Delete
end if
LogoWin.show
LogoWin.WriteToSTDOUT (EndofLine+EndofLine+"Running MEME in zoops mode...")
ErrCode=MEME(alignment_tmp, MEMEf, opt+" -mod zoops")
If ErrCode=0 then
LogoWin.WriteToSTDOUT (" done."+EndofLine)
end if
'Run MEME in Zero or One per sequence' mode:
MEMEf=OutF.child("Anr")
FixPath4Windows(MEMEf)
if MEMEf<>NIL then
if MEMEf.Exists then
MEMEf.Delete
end if
LogoWin.show
LogoWin.WriteToSTDOUT ("Running MEME in anr mode...")
ErrCode=MEME(alignment_tmp, MEMEf, opt+" -mod anr")
If ErrCode=0 then
LogoWin.WriteToSTDOUT (" done."+EndofLine)
end if
LogoWin.WriteToSTDOUT (EndofLine+"Results written to "+outf.Shellpath)
else
msgbox "Can't create MEME output folder!"
'return -1
end if
else
End If
End If
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function GenomeScanCr() As Boolean Handles GenomeScanCr.Action
ScanGenomeCR
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function GenomeScanGenome() As Boolean Handles GenomeScanGenome.Action
ScanGenome
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function HelpHMMERuserguide() As Boolean Handles HelpHMMERuserguide.Action
dim f as FolderItem
f=Resources_f.child("HmmerUserGuide.pdf")
if f<>nil AND f.exists then
f.Launch
end if
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function HelpHMMERWebSite() As Boolean Handles HelpHMMERWebSite.Action
HelpWin.LoadPage("http://hmmer.org")
HelpWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function HelpMEMEhelp() As Boolean Handles HelpMEMEhelp.Action
HelpWin.LoadPage("http://meme-suite.org")
HelpWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function HelpSigmoIDHelp() As Boolean Handles HelpSigmoIDHelp.Action
dim f As folderitem
f=Resources_f.Child("Help").child(kHelpFileName)
if f<>nil then
if f.exists then
HelpWin.show
HelpWin.LoadPage(f)
end if
else
f=Resources_f.Child("Help").child("help_en.html")
if f<>nil then
if f.exists then
HelpWin.show
HelpWin.LoadPage(f)
end if
end if
end if
End Function
#tag EndMenuHandler
#tag MenuHandler
Function RegPreciseRegulogs() As Boolean Handles RegPreciseRegulogs.Action
RegPreciseWin.title="RegPrecise: regulogs"
RegPreciseWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function RegPreciseRegulons() As Boolean Handles RegPreciseRegulons.Action
RegPreciseWin.title="RegPrecise: regulons"
RegPreciseWin.LoadGenomes
RegPreciseWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function RegulonCollecTF() As Boolean Handles RegulonCollecTF.Action
CollecTFwin.CollecTFfile=Resources_f.child("collectf_export.tsv")
if CollecTFWin.CollecTFfile<>Nil and CollecTFWin.CollecTFfile.Exists then
CollecTFWin.show
CollecTFWin.FillRegulatorList(CollecTFWin.CollecTFfile)
else
LogoWin.WriteToSTDOUT("CollecTF data file is missing")
end if
End Function
#tag EndMenuHandler
#tag MenuHandler
Function RegulonLocalMotifCollections() As Boolean Handles RegulonLocalMotifCollections.Action
LocalMotifCollectionsWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function RegulonRegPreciseTFFamilies() As Boolean Handles RegulonRegPreciseTFFamilies.Action
'RegPreciseWin.title="RegPrecise: regulons"
RegPreciseTFcollectionsWin.LoadFamilies
RegPreciseTFcollectionsWin.show
Return True
End Function
#tag EndMenuHandler
#tag MenuHandler
Function RegulonTomTom() As Boolean Handles RegulonTomTom.Action
TomTomWin.show
Return True
End Function
#tag EndMenuHandler
#tag Method, Flags = &h0
Sub ChipMdata2Logo()
Dim f As FolderItem
Dim openF As OpenDialog
dim tis As TextInputStream
Dim fasta, chipMout, winTitle As String
dim seqid,fastaid(), motifs(),anrsites() As string
dim word As new RegEx
dim occs As new RegEx
dim id As new RegEx
dim rgm As RegExMatch
dim s As Site
dim m As Motif
Dim w As ChipMLogo
dim snum As integer
word.SearchPattern="(^WORD\|)(\d+)(\t\d+\t)(\w+)(\t\S+\t)(\w+)"
occs.SearchPattern="(^OCCS\|\d+\;)(\d+)(\;\s)(.*)"
id.SearchPattern="^\>.*"
openF = new OpenDialog
openF.Title="Open ChipMunk result"
openF.promptText="Select file with ChipMunk output"
openF.Title="Open alignment"
'openF.Filter=FileTypes.Text
f = openF.ShowModal
If f <>Nil Then
tis = TextInputStream.Open(f)
chipMout=tis.ReadAll
tis.Close
winTitle=f.DisplayName
end if
// Try to find ChipMunk input from the command stored in the result file
' the filename should go after ' s:' and can include full path
Dim chipMfileName As String
Dim chipMfile As folderitem
Dim dataSet As String
If InStr(chipMout, " s:")>0 Then
dataSet=" s:" 'simple multi-fasta
Elseif InStr(chipMout, " w:")>0 Then
dataSet=" w:" 'weighted data set
Elseif InStr(chipMout, " p:")>0 Then
dataSet=" p:" 'peak data with the positional preferences profile
Elseif InStr(chipMout, " m:")>0 Then
dataSet=" m:" 'peak summit mode
Else
MsgBox "Can't guess dataset format."
Exit 'smth wrong with the file!
End If
chipMfileName=NthField(chipMout, dataSet, 2)
chipMfileName=ReplaceAll(chipMfileName, "\ ", "\\\") 'mask escaped spaces in filename
chipMfileName=NthField(chipMfileName, " ",1)
If InStr(chipMfileName, "/")>0 Then 'hopefully full path
chipMfileName=ReplaceAll(chipMfileName, "\\\", "\ ") 'restore escaped path
chipMfile=GetFolderItem(chipMfileName,FolderItem.PathTypeShell)
Else 'filename only
'assume input file is in the same dir as output
chipMfileName=ReplaceAll(chipMfileName, "\\\", " ") 'restore spaces in filename
If f <>Nil Then
chipMfile=f.Parent.child(chipMfileName)
End If
End If
if instr(chipMout,"MOTF|")=0 and InStr(chipMout,"WORD|")>0 then 'probably file with single motif produced by plain ChIPMunk, so load logo strait to the main window
dim chiplogo as String = ""
rgm=word.Search(chipMout)
do
if rgm<>nil then
chiplogo=chiplogo+">"+rgm.SubExpressionString(2)+" "+rgm.SubExpressionString(6)+EndOfLine.UNIX+rgm.SubExpressionString(4)+EndOfLine.UNIX
end if
rgm=word.search
loop until rgm=nil
f=TemporaryFolder.child("chiplogodata")
if f<>nil then
if f.Exists then f.Delete
dim outstream As TextOutputStream
outstream = TextOutputStream.Create(f)
outstream.Write(ConvertEncoding(chiplogo, Encodings.UTF8))
outstream.Close
LogoWin.LoadAlignment(f)
else
msgbox "Can't write converted file."
end if
else
chipMfileName=NthField(chipMout, dataSet, 2)
chipMfileName=ReplaceAll(chipMfileName, "\ ", "\\\") 'mask escaped spaces in filename
chipMfileName=NthField(chipMfileName, " ",1)
If InStr(chipMfileName, "/")>0 Then 'hopefully full path
chipMfileName=ReplaceAll(chipMfileName, "\\\", "\ ") 'restore escaped path
chipMfile=GetFolderItem(chipMfileName,FolderItem.PathTypeShell)
Else 'filename only
'assume input file is in the same dir as output
chipMfileName=ReplaceAll(chipMfileName, "\\\", " ") 'restore spaces in filename
If f <>Nil Then
chipMfile=f.Parent.child(chipMfileName)
End If
End If
If chipMfile=Nil Or (chipMfile<>Nil And (Not chipMfile.Exists)) Then
openF = New OpenDialog
openF.Title="Open fasta file"
openF.promptText="Select file with sequences used as ChipMunk input"
openF.Filter=FileTypes.Fasta
chipMfile = openF.ShowModal
End If
If chipMfile <>Nil Then
tis = TextInputStream.Open(chipMfile)
fasta=tis.ReadAll
tis.Close
rgm=id.Search(fasta)
End If
do
if rgm<>nil then
fastaid.Append(rgm.SubExpressionString(0))
end if
rgm=id.search
loop until rgm=nil
motifs=chipMout.Split("MOTF|")
w = new ChipMLogo
for i as integer=1 to UBound(motifs)
rgm = word.search(motifs(i))
m = new Motif
do
if rgm<> NIl then
s=new Site
snum=val(trim(rgm.SubExpressionString(2)))
s.id=fastaid(snum)
s.seq=rgm.SubExpressionString(4)
s.qualValue=val(rgm.SubExpressionString(5))
s.qualValue=Floor(s.qualValue*100)/100
s.strand=rgm.SubExpressionString(6)
m.Sites.Append(s)
end
rgm=word.search
loop until rgm = nil
m.number=i
m.type="ZOOPS"
dim valrange() as double
for Each c as Site in m.Sites
valrange.Append(c.qualValue)
next
valrange.Sort
m.valrange=str(valrange(0))+" - "+str(valrange(UBound(valrange)))
w.Motifs.Append(m)
//append Zoops motif
rgm=occs.search(motifs(i))
m = new Motif
do
if rgm<> NIl then
snum=val(trim(rgm.SubExpressionString(2)))
seqid=fastaid(snum)
anrsites=split(rgm.SubExpressionString(4)," ")
for k as integer=0 to UBound(anrsites)
s=new Site
s.id=seqid
s.seq=NthField(anrsites(k),":",1)
s.qualValue=(val(NthField(anrsites(k),":",4)))
s.qualValue=Floor(s.qualValue*100)/100
s.strand=NthField(anrsites(k),":",3)
m.Sites.Append(s)
next
end
rgm=occs.search
loop until rgm = nil
m.number=i
m.type="ANR"
redim valrange(-1)
for Each c as Site in m.Sites
valrange.Append(c.qualValue)
next
valrange.Sort
m.valrange=str(valrange(0))+" - "+str(valrange(UBound(valrange)))
w.Motifs.Append(m)
//append ANR motif
next
w.populateListbox
w.Title="Motif Logos for " + winTitle
w.Visible=True
end
Exception err
If err IsA OutOfBoundsException Then
MsgBox "Can't match original sequence names with ChipMunk motif numbers. Please make sure the correct input file exists in the location specified in the ChipMunk result file you are trying to open."
Else
ExceptionHandler(err,"App:ChipMdata2Logo")
End If
End Sub
#tag EndMethod
#tag Method, Flags = &h0
Sub MakeSigFile(SigFolder as folderitem)
'structure of a transcription factor-specific folder:
'TF (folder)
'TF.fasta - alignment (fasta)
'TF.options - HmmGen, nhmmer, etc. options
'TF.info - references for the binding site data and description of the protein
'TF.hmm - calibrated hmm profile
'TF.logodata - data from weblogo in case it's not installed
'meme.txt - MEME output file in text format (optional)
'if weblogo i present, .logodata isn't required when creating .sig file
'put nhmmer options required for calibration into the .options file?
'Options for Model-specific Score Thresholding
'Curated profile databases may define specific bit score thresholds for each profile, superseding any thresh- olding based on statistical significance alone. To use these options, the profile must contain the appropriate (GA, TC, and/or NC) optional score threshold annotation; this is picked up by hmmbuild from Stockholm format alignment files. For a nucleotide model, each thresholding option has a single per-hit threshold <x> This acts as if -T<x> --incT<x> has been applied specifically using each model’s curated thresholds.
'--cut ga Use the GA (gathering) bit score threshold in the model to set per-hit reporting and
'inclusion thresholds. GA thresholds are generally considered to be the reliable curated
'thresholds defining family membership; for example, in Dfam, these thresholds are applied
'when annotating a genome with a model of a family known to be found in that organism.
'They may allow for minimal expected false discovery rate.
'--cut nc Use the NC (noise cutoff) bit score threshold in the model to set per-hit reporting and
'inclusion thresholds. NC thresholds are less stringent than GA; in the context of Pfam,
'they are generally used to store the score of the highest-scoring known false positive.
'--cut tc Use the NC (trusted cutoff) bit score threshold in the model to set per-hit reporting and
'inclusion thresholds. TC thresholds are more stringent than GA, and are generally considered
'to be the score of the lowest-scoring known true positive that is above all known false
'positives; for example, in Dfam, these thresholds are applied when annotating a genome
'with a model of a family not known to be found in that organism.
' STOCKHOLM header:
'# STOCKHOLM 1.0
'#=GF GA <Gathering threshold>
'seq1 ACDEF...GHIKL
'seq2 ACDEF...GHIKL
'seq3 ...EFMNRGHIKL
'seq1 MNPQTVWY
'seq2 MNPQTVWY
'seq3 MNPQT...
'//
Dim SigFile as FolderItem
Dim SigFileVV As VirtualVolume
'Read options:
dim optionsFile As FolderItem = SigFolder.Child(sigfolder.displayname+".options")
if optionsFile<>Nil AND optionsFile.Exists then
dim instream as TextInputStream
dim aline, cutoffs As string
'read profile calibration values
InStream = optionsFile.OpenAsTextFile
while not InStream.EOF
aLine=InStream.readLine
if left(aLine,7)="#=GF GA" then
cutoffs=cutoffs+aline+EndOfLine
elseif left(aLine,7)="#=GF NC" then
cutoffs=cutoffs+aline+EndOfLine
elseif left(aLine,7)="#=GF TC" then
cutoffs=cutoffs+aline+EndOfLine
end if
wend
dim Options as string
Options=instream.ReadAll 'Options are later scanned for the -p switch
instream.close
if cutoffs="" then
Msgbox "No cutoff settings were found in the .options file. Can't make calibrated profile without it."
return
else
'cutoffs are hopefully read, convert the alignment to Stockholm format and store it in the temp file
dim stock as FolderItem = TemporaryFolder.child("stock")
if stock <> nil then
dim AlignmentFile,rcAlignmentFile as FolderItem
'check if the site is marked as palindromic
if options.InStr("HmmGen.-p")>0 then 'reverse complement every site
AlignmentFile= SigFolder.child(sigfolder.displayname+".fasta")
if AlignmentFile<>Nil AND AlignmentFile.Exists then
rcAlignmentFile=TemporaryFolder.child("rcAliFile")
RevCompAlignment(AlignmentFile,rcAlignmentFile,true)
AlignmentFile=rcAlignmentFile
end if
else 'just open existing alignment:
AlignmentFile= SigFolder.child(sigfolder.displayname+".fasta")