Automator services for frequent bioinformatics tasks

Count Nucleotides.scpt

--What is this: This is an applescript to use in an automator service that allows you to get the nucleotide and alignment length of a sequence, along with stats on the numbers of individual characters.
--Purpose: Determine the length of a selected nucleotide and alignment string in any application.
--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Select a nucleotide string (newlines, numbers, spaces, and any other character are allowed). 2. Right-click the selection and select this service.
--Author: Robert Leach, Genomics Group, Princeton, rleach@princeton.edu

--Note, this counts "DNA characters"

on run {input, parameters}
	tell application "System Events"
		set _appname to name of first process whose frontmost is true
	end tell
	set msg to countNucleotides(input as string)
	tell application _appname
		display alert "" & msg
	end tell
	return input
end run

on countNucleotides(dnaStr)
	set astid to AppleScript's text item delimiters
	
	set AppleScript's text item delimiters to "A"
	set aCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "T"
	set tCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "G"
	set gCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "C"
	set cCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to "B"
	set bCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "D"
	set dCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "H"
	set hCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "V"
	set vCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "R"
	set rCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "Y"
	set yCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "K"
	set kCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "M"
	set mCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "S"
	set sCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "W"
	set wCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "N"
	set nCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to "-"
	set gapCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to astid
	
	
	set seqTotal to aCount + tCount + gCount + cCount + bCount + dCount + hCount + vCount + rCount + yCount + kCount + mCount + sCount + wCount + nCount
	set alnTotal to seqTotal + gapCount
	set realTotal to aCount + tCount + gCount + cCount
	set ambigTotal to seqTotal - realTotal
	
	set statsstr to "Sequence length: " & (seqTotal as string) & "

Alignment length: " & (alnTotal as string) & "

Discrete Nucleotides: " & (realTotal as string) & "

Ambiguous Nucleotides: " & (ambigTotal as string) & "

Breakdown:
	A " & aCount & "
	T " & tCount & "
	G " & gCount & "
	C " & cCount & "
"
	if bCount > 0 then
		set statsstr to statsstr & "	B " & bCount & "
"
	end if
	if dCount > 0 then
		set statsstr to statsstr & "	D " & dCount & "
"
	end if
	if hCount > 0 then
		set statsstr to statsstr & "	H " & hCount & "
"
	end if
	if vCount > 0 then
		set statsstr to statsstr & "	V " & vCount & "
"
	end if
	if rCount > 0 then
		set statsstr to statsstr & "	R " & rCount & "
"
	end if
	if yCount > 0 then
		set statsstr to statsstr & "	Y " & yCount & "
"
	end if
	if kCount > 0 then
		set statsstr to statsstr & "	K " & kCount & "
"
	end if
	if mCount > 0 then
		set statsstr to statsstr & "	M " & mCount & "
"
	end if
	if sCount > 0 then
		set statsstr to statsstr & "	S " & sCount & "
"
	end if
	if wCount > 0 then
		set statsstr to statsstr & "	W " & wCount & "
"
	end if
	if nCount > 0 then
		set statsstr to statsstr & "	N " & nCount & "
"
	end if
	if gapCount > 0 then
		set statsstr to statsstr & "	- " & gapCount & "
"
	end if
	
	return (statsstr)
end countNucleotides

Count Sequence Characters.scpt

--What is this: This is an applescript to use in an automator service that allows you to get the length of any sequence, not including whitespace characters.
--Purpose: Determine the length of a selected amino acid or any other pseudo-sequence string in any application.
--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Select a sequence string. 2. Right-click the selection and select this service.
--Author: Robert Leach, Genomics Group, Princeton, rleach@princeton.edu

--Note, this counts "non-whitespace characters", i.e. everything except space, tab, newline, & carriage return

on run {input, parameters}
	tell application "System Events"
		set _appname to name of first process whose frontmost is true
	end tell
	
	set selText to item 1 of input as text
	set AppleScript's text item delimiters to {space, tab, linefeed, return}
	set selText to text items of selText
	set AppleScript's text item delimiters to {}
	set selText to selText as string

	set character_count to count characters of selText
	tell application _appname
		display alert "" & character_count & " characters"
	end tell
	
	return input
end run

Guess Barcodes.scpt

--What is this: This is an applescript to use in an automator service that allows you to get the most likely barcode combinations from a series of fastq files.  It counts index sequences and looks for an order of magnitude jump in thos counts to guess the barcodes.
--Purpose: Determine the barcodes necessary to split fastq files by sample.
--Installation: Create an Automator service, select "Service receives selected [files of folders]", paste this code into a "Run AppleScript" action, and save as "Guess Barcodes.workflow".
--How to use it: 1. Right-click a fastq file and select this service ("Guess Barcodes"). 2. If no barcodes were found, click the "Edit Params" button and follow instructions
--Author: Robert Leach, Genomics Group, Princeton, rleach@princeton.edu
--Version: 2.1 (added a setting for 5' or 3' results only and tweaked the order of magnitude threshold to be slightly less stringent)
--Version History:
--  V2.0 Added the ability to count barcode combinations.
--  V1.1 fixed an issue with max_barcodes being 0 not working as intended.
--  V1.0 handled fastq files independently.

on run {input, parameters}
	
	set barcode_length to 8
	set max_barcodes to 100
	set check_n_seqs to 100000 --Set to 0 to check all or about 100000 to guess based on first million reads
	set show_max to 0 --Set to 1 to show max_barcodes per file or 0 to only show the guessed barcodes
	set barcodes_at_end to 0
	set done to false
	
	set fastqFiles to {}
	set validExtensions to {"fq", "fastq", "fastqsanger"}
	tell application "Finder"
		set delims to AppleScript's text item delimiters
		set AppleScript's text item delimiters to "."
		repeat with fqfile in input
			set theEXT to last item of (text items of ((get name of (fqfile)) as text))
			if theEXT is in validExtensions then
				set the end of fastqFiles to fqfile
			else
				display dialog "Extension " & ((name extension of (file fqfile)) as string) & " is not in validExtensions"
			end if
		end repeat
		set AppleScript's text item delimiters to delims
	end tell
	if (count fastqFiles) is equal to 0 then
		display dialog "Please select a file with a .fq, .fastq, or .fastqsanger extension"
		return
	end if
	
	repeat while done is false
		set barcodes to my getBarcodes(barcode_length, max_barcodes, check_n_seqs, show_max, fastqFiles, barcodes_at_end)
		
		tell application "System Events"
			set response to (display dialog "Educated barcode guesses:" default answer (barcodes as string) buttons {"Edit Params", "OK"} default button 1 with title "Barcodes")
		end tell
		
		if (the button returned of response) is "OK" then
			set done to true
		else
			set {barcode_length, max_barcodes, check_n_seqs, show_max, barcodes_at_end} to my displayMultiDialog("Edit Barcode Search Parameters", "Edit the parameters that were last used on each line below.  (Barcodes are determined by abundance - only the most abundant are considered.  The cutoff selected is where the abundance jumps by an order of magnitude.)", {"• Barcode Length", "• Max Barcodes to evaluate (0 = all)", "• Number of reads to process", "• Show all considered barcodes (0=No, 1=Yes)", "• Barcodes at 3' end (0=No, 1=Yes)"}, {barcode_length as string, max_barcodes as string, check_n_seqs as string, show_max as string, barcodes_at_end as string})
		end if
	end repeat
end run

on getBarcodes(barcode_length, max_barcodes, check_n_seqs, show_max, fqfiles, barcodes_at_end)
	set check_n_lines to check_n_seqs * 4
	set limit_command to "tail -n " & max_barcodes
	if max_barcodes < 1 then
		set limit_command to "cat"
	end if
	
	tell application "Finder"
		set filenames to {}
		
		set paste_command to "paste"
		
		repeat with fqfile in fqfiles
			set the end of filenames to name of fqfile
			if check_n_seqs < 1 then
				if (barcodes_at_end as integer) is equal to 0 then
					set paste_command to paste_command & " <(cat " & ((quoted form of (POSIX path of fqfile)) as string) & " | awk '(NR - 2) % 4 == 0' | perl -ne 'chomp;print(substr($_,0," & (barcode_length as string) & "),qq(\\n))')"
				else
					set paste_command to paste_command & " <(cat " & ((quoted form of (POSIX path of fqfile)) as string) & " | awk '(NR - 2) % 4 == 0' | perl -ne 'chomp;print(substr($_,-" & (barcode_length as string) & "),qq(\\n))')"
				end if
			else
				if (barcodes_at_end as integer) is equal to 0 then
					set paste_command to paste_command & " <(head -n " & check_n_lines & " " & ((quoted form of (POSIX path of fqfile)) as string) & " | awk '(NR - 2) % 4 == 0' | perl -ne 'chomp;print(substr($_,0," & (barcode_length as string) & "),qq(\\n))')"
				else
					set paste_command to paste_command & " <(head -n " & check_n_lines & " " & ((quoted form of (POSIX path of fqfile)) as string) & " | awk '(NR - 2) % 4 == 0' | perl -ne 'chomp;print(substr($_,-" & (barcode_length as string) & "),qq(\\n))')"
				end if
			end if
		end repeat
		
		if (barcodes_at_end as integer) is equal to 0 then
			set barcodes to "5' barcodes for files:" & return & return
		else
			set barcodes to "3' barcodes for files:" & return & return
		end if
		
		set barcodes to barcodes & tab & my join(return & tab, filenames) & ":" & return & "----------" & return & return
		
		set barcodes to barcodes & (do shell script "/bin/bash -s <<'EOF'" & linefeed & paste_command & " | sort | uniq -c | sort -n | " & limit_command & " | perl -e '$p=0;$o=0;while(<STDIN>){if(/(\\d+)/){$v=$1;if($o>0 && $v>(($o>10?$o-10:$o)*10)){$p=1;if(" & (show_max as string) & "){print(qq(\\n))}}s/\\s*(\\d+)\\s*(.+)\\s*/$2\\t$1\\n/;print if($p || " & (show_max as string) & ");$o=$v;}}if(!$p && !" & (show_max as string) & "){print(qq(No barcodes found. Try Editing params.))}'" & linefeed & "EOF") & return & return
		
	end tell
end getBarcodes

on displayMultiDialog(mytitle, myPrompt, valuePrompts, default_vals)
	return (inputItems for valuePrompts given title:mytitle, prompt:myPrompt, defaults:default_vals)
end displayMultiDialog

to inputItems for someItems given title:theTitle, prompt:thePrompt, defaults:theDefaults
	(*
    displays a dialog for multiple item entry - a carriage return is used between each input item
    for each item in someItems, a line of text is displayed in the dialog and a line is reserved for the input
        the number of items returned are padded or truncated to match the number of items in someItems
    to fit the size of the dialog, items should be limited in length (~30) and number (~15)  
        parameters -        someItems [list/integer]: a list or count of items to get from the dialog
                        theTitle [boolean/text]: use a default or the given dialog title
                        thePrompt [boolean/text]: use a default or the given prompt text
        returns [list]:     a list of the input items
    *)
	if thePrompt is in {true, false} then -- "with" or "without" prompt
		if thePrompt then
			set thePrompt to "Input the following items:" & return & return -- default
		else
			set thePrompt to ""
		end if
	else -- fix up the prompt a bit
		set thePrompt to thePrompt & return & return
	end if
	
	if theTitle is in {true, false} then if theTitle then -- "with" or "without" title
		set theTitle to "Multiple Input Dialog" -- default
	else
		set theTitle to ""
	end if
	
	if theDefaults is in {false} then -- "with" or "without" prompt
		set theDefaults to {}
	end if
	set theDefaultCount to (count theDefaults)
	
	if class of someItems is integer then -- no item list
		set {theCount, someItems} to {someItems, ""}
		if thePrompt is not "" then set thePrompt to text 1 thru -2 of thePrompt
	else
		set theCount to (count someItems)
	end if
	if theCount is less than 1 then error "inputItems handler:  empty input list"
	set {theItems, theInput} to {{}, {}}
	if theDefaultCount is greater than theCount then error "inputItems handler:  Too many default values"
	
	repeat with itemNum from 1 to theCount -- set the number of lines in the input and the defaults
		if itemNum is greater than theDefaultCount then
			set the end of theInput to ""
			if theDefaultCount is greater than 0 then
				set item itemNum of someItems to (item itemNum of someItems) & " [\"\"]"
			end if
		else
			set the end of theInput to item itemNum of theDefaults as string
			set item itemNum of someItems to (item itemNum of someItems) & " [\"" & (item itemNum of theDefaults) & "\"]"
		end if
	end repeat
	
	set {tempTID, AppleScript's text item delimiters} to {AppleScript's text item delimiters, return}
	set {someItems, theInput} to {someItems as text, theInput as text}
	set AppleScript's text item delimiters to tempTID
	
	set theInput to paragraphs of text returned of (display dialog thePrompt & someItems with title theTitle default answer theInput)
	
	repeat with anItem from 1 to theCount -- pad/truncate entered items
		try
			set the end of theItems to (item anItem of theInput)
		on error
			set the end of theItems to ""
		end try
	end repeat
	return theItems
end inputItems

on join(myDelimiter, myList)
	set astid to AppleScript's text item delimiters
	set AppleScript's text item delimiters to myDelimiter
	set joinedString to myList as text
	set AppleScript's text item delimiters to astid
	return joinedString
end join

Reverse Complement.scpt

--What is this: This is an applescript to use in an automator service that allows you to get the reverse complement of selected DNA sequence in a resulting dialog window.
--Purpose: To quickly get the reverse complement of a selected sequence in any app.
--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Select the sequence you wish to see the reverse complement of. 2. Right-click the selection and select this service.
--Author: Robert Leach, Genomics Group, Princeton, rleach@princeton.edu


on run {input, parameters}
	tell application "System Events"
		set _appname to name of first process whose frontmost is true
	end tell
	set msg to reverseComplement(input as string)
	tell application _appname
		display dialog "Reverse Complement:" default answer msg buttons {"OK"} default button 1 with title "Reverse Complement"
	end tell
	return input
end run

on reverseComplement(dnaStr)
	set revStr to reverse of characters of dnaStr as text
	set revCompStr to complement(revStr)
	return (revCompStr)
end reverseComplement

on complement(dnaStr)
	set str_pos to 1
	set len to length of dnaStr
	set comp to ""
	repeat while str_pos ≤ len
		set nt to text str_pos thru str_pos of dnaStr
		set comp to comp & complementNt(nt)
		set str_pos to str_pos + 1
	end repeat
	return (comp)
end complement

on complementNt(nt)
	set compNt to nt
	
	if nt is equal to "A" then
		return ("T")
	else if nt is equal to "a" then
		return ("t")
	else if nt is equal to "T" then
		return ("A")
	else if nt is equal to "t" then
		return ("a")
	else if nt is equal to "G" then
		return ("C")
	else if nt is equal to "g" then
		return ("c")
	else if nt is equal to "C" then
		return ("G")
	else if nt is equal to "c" then
		return ("g")
	else if nt is equal to "B" then
		return ("V")
	else if nt is equal to "b" then
		return ("v")
	else if nt is equal to "D" then
		return ("H")
	else if nt is equal to "d" then
		return ("h")
	else if nt is equal to "H" then
		return ("D")
	else if nt is equal to "h" then
		return ("d")
	else if nt is equal to "V" then
		return ("B")
	else if nt is equal to "v" then
		return ("b")
	else if nt is equal to "R" then
		return ("Y")
	else if nt is equal to "r" then
		return ("y")
	else if nt is equal to "Y" then
		return ("R")
	else if nt is equal to "y" then
		return ("r")
	else if nt is equal to "K" then
		return ("M")
	else if nt is equal to "k" then
		return ("m")
	else if nt is equal to "M" then
		return ("K")
	else if nt is equal to "m" then
		return ("k")
	end if
	
	--Don't need to do S, W, or N, because they complement themselves
	--All other characters such as white spaces, numbers, gaps or other stuff will just be returned as-is without error or warning
	
	return (compNt)
end complementNt

Select N Alignment Characters.scpt

--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Copy a number indicating the length you want the selection to be. 2. Select the region of text where you want the copied length to be selected. 3. Right-click the selection and select this service.

--NOTES:
--If the contents of the clipboard is not a number, you'll be prompted to enter a length.
--If the selected text is in Terminal.app, the modified selection will display in a dialog window (because the arrow keys are used for the selection modification and that doesn't work in Terminal).  Also, if the target selection length is longer than the current selection, an error about selection length will be displayed.
--If input is not supplied, this script will backup the current clipboard, copy the current selection to get the currently selected text, then restore the clipboard.

on run {input, parameters}
	
	try
		set debug to false
		if input's class is not list then
			set input to (my getHighlight(debug))
		end if
		
		tell application "System Events"
			--See if the clipboard has a number in it to use for the selection length
			set checkClipboard to the clipboard as text
			if my isNumString(checkClipboard) then
				set n to checkClipboard as integer
			else
				--Get the name of the frontmost application so we can bring the front window back into focus after the dialog window goes away (which surprisingly, is not the default behavior)
				set curProc to (name of first process whose frontmost is true)
				
				set n to my getintvalue()
				
				--And this is the only trick I've found to bring any window in an app back into focus
				do shell script "open -a '" & (curProc as string) & "'"
				delay 0.2
			end if
			
			set {selText, nt_count} to (my selectAtLeastAln((input as string), (n as integer), debug))
			
			--Exit if an empty string was returned (indicating an error)
			if selText is "" then
				return
			end if
			
			--Estimate/guess whether it will be quicker to shrink the selection from the end or grow the selection from the beginning
			set shrinkit to ((nt_count - n) < n)
			
			--Figure out whether the selection must be lengthened or shrunk
			if nt_count is equal to 0 or n is greater than nt_count then
				display dialog "The selection length must be greater than the number of characters to select"
				return
			end if
			
			--See if we're in Terminal
			set isTerminal to ((name of first process where it is frontmost) as string) is equal to "Terminal"
			
			if isTerminal is true then
				ignoring application responses
					display dialog "Length " & n & " is selected below:" default answer selText buttons {"OK"} default button 1 with title "Selected Character Position"
				end ignoring
			end if
			
			if shrinkit is false then
				key code 123
				set str_pos to 1
				set nt_count to 0
				repeat while nt_count < n
					key code 124 using {shift down}
					set nt to text str_pos thru str_pos of selText
					if (my countAlignChars(nt)) > 0 then
						set nt_count to nt_count + 1
					end if
					set str_pos to str_pos + 1
				end repeat
			else
				--Trick to make sure arrow presses affect the right side of the selection instead of the left
				set character_count to count characters of selText
				key code 124 using {shift down}
				key code 123 using {shift down}
				if (count characters of selText) < character_count then
					key code 124 using {shift down}
				end if
				
				set str_pos to character_count
				set nt to text str_pos thru str_pos of selText
				repeat while nt_count > n or (my countAlignChars(nt)) < 1
					key code 123 using {shift down}
					if (my countAlignChars(nt)) > 0 then
						set nt_count to nt_count - 1
					end if
					set str_pos to str_pos - 1
					set nt to text str_pos thru str_pos of selText
				end repeat
			end if
			delay 1
		end tell
	on error errstr
		display dialog errstr
	end try
	
end run



property mytitle : "Length of text to select"

-- I am asking the user to provide an integer
-- In case the user cancels the dialog, I return «missing value»
on getintvalue()
	set dlgmsg to "How many characters would you like to select?:"
	try
		display dialog dlgmsg default answer "1" buttons {"Cancel", "Enter"} default button 2 with title mytitle
	on error
		-- User canceled
		return missing value
	end try
	set dlgresult to result
	set usrinput to text returned of dlgresult
	-- the user did not enter anything...
	if usrinput is "" then
		my getintvalue()
	else
		-- let's check if the user entered numbers only
		set nums to {"1", "2", "3", "4", "5", "6", "7", "8", "9", "0"}
		set invalidchars to ""
		repeat with char in usrinput
			if char is not in nums then
				set invalidchars to invalidchars & char & space
			end if
		end repeat
		-- we found invalid characters
		if invalidchars is not "" then
			set errmsg to "We found the following characters in the given input. Please enter numbers only." & return & return & invalidchars & return
			my dsperrmsg(errmsg, "--")
			my getintvalue()
		else
			-- let's try to transform the user input into an integer
			try
				set intvalue to usrinput as integer
				return intvalue
			on error
				set errmsg to "We could not coerce the given input into an integer:" & return & return & usrinput & return
				my dsperrmsg(errmsg, "--")
				my getintvalue()
			end try
		end if
	end if
end getintvalue

-- I am displaying error messages to the user
on dsperrmsg(errmsg, errnum)
	tell me
		activate
		display dialog errmsg & " (" & errnum & ")" buttons {"OK"} default button 1 with title mytitle with icon stop
	end tell
end dsperrmsg

-- isNumString :: String -> Bool
on isNumString(s)
	try
		if class of s is string then
			set c to class of (s as number)
			c is real or c is integer
		else
			false
		end if
	on error
		false
	end try
end isNumString

on getHighlight(debug)
	
	--Save the current contents of the clipboard
	try
		set theSpare to the clipboard --as text
	on error
		set response to (display dialog "Warning: The contents of the clipboard will be lost." buttons {"Cancel", "OK"})
		if button returned of response is "OK" then
			set theSpare to ""
		end if
	end try
	set the clipboard to ""
	--Declare the variable we're going to return
	set selecTxt to ""
	
	tell application "System Events"
		--Initiate the copy
		keystroke "c" using {command down}
		
		--Wait up to 2 seconds for the copy to finish
		set done to "no"
		set waitnum to 0
		set waitInterval to 0.02
		set maxwaits to 100
		
		--Repeat while the clipboard contents have not changed
		repeat while done = "no"
			--Get the contents of the clipboard
			try
				set selecTxt to the clipboard as text
			end try
			
			--See if we're done or need to wait
			if waitnum is equal to maxwaits then
				set done to "yes"
			else if selecTxt is equal to "" then
				delay waitInterval
				set waitnum to waitnum + 1
			else
				set done to "yes"
			end if
			
		end repeat
		
		if debug is true then
			try
				display dialog "Copied text: " & (the clipboard as text)
			end try
		end if
	end tell
	
	--Restore the original clipboard contents
	set the clipboard to theSpare --as record
	
	if debug is true then
		try
			display dialog "The clipboard contents have been restored to " & (the clipboard as text)
		end try
	end if
	
	--Return the highlighted text
	return selecTxt
	
end getHighlight

on countAlignChars(dnaStr)
	set astid to AppleScript's text item delimiters
	
	set AppleScript's text item delimiters to "A"
	set aCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "T"
	set tCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "G"
	set gCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "C"
	set cCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to "B"
	set bCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "D"
	set dCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "H"
	set hCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "V"
	set vCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "R"
	set rCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "Y"
	set yCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "K"
	set kCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "M"
	set mCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "S"
	set sCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "W"
	set wCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "N"
	set nCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to "-"
	set gapCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to astid
	
	
	set seqTotal to aCount + tCount + gCount + cCount + bCount + dCount + hCount + vCount + rCount + yCount + kCount + mCount + sCount + wCount + nCount
	set alnTotal to seqTotal + gapCount
	
	
	return (alnTotal as integer)
end countAlignChars

--Uses the down arrow to grab at least n characters of nucleotides and returns the newly selected string and the number of nucleotides it contains
on selectAtLeastAln(initial_str as string, n as integer, debug)
	
	set cur_str to initial_str
	set character_count to ((count characters of cur_str) as integer)
	set last_character_count to 0
	set nt_count to ((my countAlignChars(cur_str)) as integer)
	repeat while character_count > last_character_count and nt_count < n
		--Add a line to the selection
		tell application "System Events" to key code 125 using {shift down}
		set cur_str to (my getHighlight(debug))
		set last_character_count to character_count
		set character_count to ((count characters of cur_str) as integer)
		set nt_count to (my countAlignChars(cur_str))
	end repeat
	if nt_count < n then
		display dialog "Error: Unable to select enough sequence. Please make sure to select more sequence than the target length (" & (n as string) & ")."
		return ({"", 0})
	end if
	return ({cur_str as string, nt_count as integer})
end selectAtLeastAln

Select N Characters.scpt

--What is this: This is an applescript to use in an automator service that allows you to modify the length of a text selection to a value specified (either by a number on the clipboard or a number entered at a prompt).
--Purpose: The initial intent is to use this service to visualize a specific position in a DNA or protein string (although it currently assumes the string is solid sequence characters - a future *separate* version will count only relevant characters).
--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Copy a number indicating the length you want the selection to be. 2. Select the region of text where you want the copied length to be selected. 3. Right-click the selection and select this service.
--Author: Robert Leach, Genomics Group, Princeton, rleach@princeton.edu

--NOTES:
--If the contents of the clipboard is not a number, you'll be prompted to enter a length.
--If the selected text is in Terminal.app, the modified selection will display in a dialog window (because the arrow keys are used for the selection modification and that doesn't work in Terminal).  Also, if the target selection length is longer than the current selection, the remainder will be filled in with N's (because this was originally made for DNA strings).
--If input is not supplied, this script will backup the current clipboard, copy the current selection to get the currently selected text, then restore the clipboard.

on run {input, parameters}
	
	try
		set debug to false
		if input's class is not list then
			set input to getHighlight(debug)
		end if
		
		tell application "System Events"
			--See if the clipboard has a number in it to use for the selection length
			set checkClipboard to the clipboard as text
			if my isNumString(checkClipboard) then
				set n to checkClipboard as integer
			else
				--Get the name of the frontmost application so we can bring the front window back into focus after the dialog window goes away (which surprisingly, is not the default behavior)
				set curProc to (name of first process whose frontmost is true)
				
				set n to my getintvalue()
				
				--And this is the only trick I've found to bring any window in an app back into focus
				do shell script "open -a '" & (curProc as string) & "'"
				delay 0.2
			end if
			
			--Check the length of the selected text passed in
			set character_count to count characters of ((input as string) as string)
			
			set lengthen to false
			set mod_length to character_count - n
			--Figure out whether the selection must be lengthened or shrunk
			if character_count is equal to 0 or n is greater than character_count then
				set lengthen to true
				set mod_length to n - character_count
			end if
			
			--See if we're in Terminal
			set isTerminal to ((name of first process where it is frontmost) as string) is equal to "Terminal"
			
			if isTerminal is true then
				if lengthen is true then
					set substr to (input as string)
					repeat mod_length times
						set substr to substr & "N"
					end repeat
				else
					set substr to text 1 thru n of (input as string)
					set substr to substr & (text (n + 1) thru character_count of (input as string))
				end if
				ignoring application responses
					display dialog "Length " & n & " is selected below:" default answer substr buttons {"OK"} default button 1 with title "Selected Character Position"
				end ignoring
			end if
			
			--Trick to make sure arrow presses affect the right side of the selection instead of the left
			if not (character_count is equal to 0 or n is greater than character_count) then
				key code 124 using {shift down}
				key code 123 using {shift down}
				key code 124 using {shift down}
			end if
			
			if lengthen is false and n is less than mod_length then
				if character_count is greater than 0 then
					key code 123
				end if
				repeat n times
					key code 124 using {shift down}
				end repeat
			else
				repeat mod_length times
					if lengthen is true then
						key code 124 using {shift down}
					else
						key code 123 using {shift down}
					end if
				end repeat
			end if
			delay 1
		end tell
	on error errstr
		display dialog errstr
	end try
	
end run



property mytitle : "Length of text to select"

-- I am asking the user to provide an integer
-- In case the user cancels the dialog, I return «missing value»
on getintvalue()
	set dlgmsg to "How many characters would you like to select?:"
	try
		display dialog dlgmsg default answer "1" buttons {"Cancel", "Enter"} default button 2 with title mytitle
	on error
		-- User canceled
		return missing value
	end try
	set dlgresult to result
	set usrinput to text returned of dlgresult
	-- the user did not enter anything...
	if usrinput is "" then
		my getintvalue()
	else
		-- let's check if the user entered numbers only
		set nums to {"1", "2", "3", "4", "5", "6", "7", "8", "9", "0"}
		set invalidchars to ""
		repeat with char in usrinput
			if char is not in nums then
				set invalidchars to invalidchars & char & space
			end if
		end repeat
		-- we found invalid characters
		if invalidchars is not "" then
			set errmsg to "We found the following characters in the given input. Please enter numbers only." & return & return & invalidchars & return
			my dsperrmsg(errmsg, "--")
			my getintvalue()
		else
			-- let's try to transform the user input into an integer
			try
				set intvalue to usrinput as integer
				return intvalue
			on error
				set errmsg to "We could not coerce the given input into an integer:" & return & return & usrinput & return
				my dsperrmsg(errmsg, "--")
				my getintvalue()
			end try
		end if
	end if
end getintvalue

-- I am displaying error messages to the user
on dsperrmsg(errmsg, errnum)
	tell me
		activate
		display dialog errmsg & " (" & errnum & ")" buttons {"OK"} default button 1 with title mytitle with icon stop
	end tell
end dsperrmsg

-- isNumString :: String -> Bool
on isNumString(s)
	try
		if class of s is string then
			set c to class of (s as number)
			c is real or c is integer
		else
			false
		end if
	on error
		false
	end try
end isNumString

on getHighlight(debug)
	
	--Save the current contents of the clipboard
	try
		set theSpare to the clipboard --as text
	on error
		set response to (display dialog "Warning: The contents of the clipboard will be lost." buttons {"Cancel", "OK"})
		if button returned of response is "OK" then
			set theSpare to ""
		end if
	end try
	set the clipboard to ""
	--Declare the variable we're going to return
	set selecTxt to ""
	
	tell application "System Events"
		--Initiate the copy
		keystroke "c" using {command down}
		
		--Wait up to 2 seconds for the copy to finish
		set done to "no"
		set waitnum to 0
		set waitInterval to 0.02
		set maxwaits to 100
		
		--Repeat while the clipboard contents have not changed
		repeat while done = "no"
			--Get the contents of the clipboard
			try
				set selecTxt to the clipboard as text
			end try
			
			--See if we're done or need to wait
			if waitnum is equal to maxwaits then
				set done to "yes"
			else if selecTxt is equal to "" then
				delay waitInterval
				set waitnum to waitnum + 1
			else
				set done to "yes"
			end if
			
		end repeat
		
		if debug is true then
			try
				display dialog "Copied text: " & (the clipboard as text)
			end try
		end if
	end tell
	
	--Restore the original clipboard contents
	set the clipboard to theSpare --as record
	
	if debug is true then
		try
			display dialog "The clipboard contents have been restored to " & (the clipboard as text)
		end try
	end if
	
	--Return the highlighted text
	return selecTxt
	
end getHighlight

Select N Nucleotides.scpt

--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Copy a number indicating the length you want the selection to be. 2. Select the region of text where you want the copied length to be selected. 3. Right-click the selection and select this service.

--NOTES:
--If the contents of the clipboard is not a number, you'll be prompted to enter a length.
--If the selected text is in Terminal.app, the modified selection will display in a dialog window (because the arrow keys are used for the selection modification and that doesn't work in Terminal).  Also, if the target selection length is longer than the current selection, an error about selection length will be displayed.
--If input is not supplied, this script will backup the current clipboard, copy the current selection to get the currently selected text, then restore the clipboard.

on run {input, parameters}
	
	try
		set debug to false
		if input's class is not list then
			set input to (my getHighlight(debug))
		end if
		
		tell application "System Events"
			--See if the clipboard has a number in it to use for the selection length
			set checkClipboard to the clipboard as text
			if my isNumString(checkClipboard) then
				set n to checkClipboard as integer
			else
				--Get the name of the frontmost application so we can bring the front window back into focus after the dialog window goes away (which surprisingly, is not the default behavior)
				set curProc to (name of first process whose frontmost is true)
				
				set n to my getintvalue()
				
				--And this is the only trick I've found to bring any window in an app back into focus
				do shell script "open -a '" & (curProc as string) & "'"
				delay 0.2
			end if
			
			set {selText, nt_count} to (my selectAtLeast((input as string), (n as integer), debug))
			
			--Exit if an empty string was returned (indicating an error)
			if selText is "" then
				return
			end if
			
			--Estimate/guess whether it will be quicker to shrink the selection from the end or grow the selection from the beginning
			set shrinkit to ((nt_count - n) < n)
			
			--Figure out whether the selection must be lengthened or shrunk
			if nt_count is equal to 0 or n is greater than nt_count then
				display dialog "The selection length must be greater than the number of characters to select"
				return
			end if
			
			--See if we're in Terminal
			set isTerminal to ((name of first process where it is frontmost) as string) is equal to "Terminal"
			
			if isTerminal is true then
				ignoring application responses
					display dialog "Length " & n & " is selected below:" default answer selText buttons {"OK"} default button 1 with title "Selected Character Position"
				end ignoring
			end if
			
			if shrinkit is false then
				key code 123
				set str_pos to 1
				set nt_count to 0
				repeat while nt_count < n
					key code 124 using {shift down}
					set nt to text str_pos thru str_pos of selText
					if (my countNucleotides(nt)) > 0 then
						set nt_count to nt_count + 1
					end if
					set str_pos to str_pos + 1
				end repeat
			else
				--Trick to make sure arrow presses affect the right side of the selection instead of the left
				set character_count to count characters of selText
				key code 124 using {shift down}
				key code 123 using {shift down}
				if (count characters of selText) < character_count then
					key code 124 using {shift down}
				end if
				
				set str_pos to character_count
				set nt to text str_pos thru str_pos of selText
				repeat while nt_count > n or (my countNucleotides(nt)) < 1
					key code 123 using {shift down}
					if (my countNucleotides(nt)) > 0 then
						set nt_count to nt_count - 1
					end if
					set str_pos to str_pos - 1
					set nt to text str_pos thru str_pos of selText
				end repeat
			end if
			delay 1
		end tell
	on error errstr
		display dialog errstr
	end try
	
end run



property mytitle : "Length of text to select"

-- I am asking the user to provide an integer
-- In case the user cancels the dialog, I return «missing value»
on getintvalue()
	set dlgmsg to "How many characters would you like to select?:"
	try
		display dialog dlgmsg default answer "1" buttons {"Cancel", "Enter"} default button 2 with title mytitle
	on error
		-- User canceled
		return missing value
	end try
	set dlgresult to result
	set usrinput to text returned of dlgresult
	-- the user did not enter anything...
	if usrinput is "" then
		my getintvalue()
	else
		-- let's check if the user entered numbers only
		set nums to {"1", "2", "3", "4", "5", "6", "7", "8", "9", "0"}
		set invalidchars to ""
		repeat with char in usrinput
			if char is not in nums then
				set invalidchars to invalidchars & char & space
			end if
		end repeat
		-- we found invalid characters
		if invalidchars is not "" then
			set errmsg to "We found the following characters in the given input. Please enter numbers only." & return & return & invalidchars & return
			my dsperrmsg(errmsg, "--")
			my getintvalue()
		else
			-- let's try to transform the user input into an integer
			try
				set intvalue to usrinput as integer
				return intvalue
			on error
				set errmsg to "We could not coerce the given input into an integer:" & return & return & usrinput & return
				my dsperrmsg(errmsg, "--")
				my getintvalue()
			end try
		end if
	end if
end getintvalue

-- I am displaying error messages to the user
on dsperrmsg(errmsg, errnum)
	tell me
		activate
		display dialog errmsg & " (" & errnum & ")" buttons {"OK"} default button 1 with title mytitle with icon stop
	end tell
end dsperrmsg

-- isNumString :: String -> Bool
on isNumString(s)
	try
		if class of s is string then
			set c to class of (s as number)
			c is real or c is integer
		else
			false
		end if
	on error
		false
	end try
end isNumString

on getHighlight(debug)
	
	--Save the current contents of the clipboard
	try
		set theSpare to the clipboard --as text
	on error
		set response to (display dialog "Warning: The contents of the clipboard will be lost." buttons {"Cancel", "OK"})
		if button returned of response is "OK" then
			set theSpare to ""
		end if
	end try
	set the clipboard to ""
	--Declare the variable we're going to return
	set selecTxt to ""
	
	tell application "System Events"
		--Initiate the copy
		keystroke "c" using {command down}
		
		--Wait up to 2 seconds for the copy to finish
		set done to "no"
		set waitnum to 0
		set waitInterval to 0.02
		set maxwaits to 100
		
		--Repeat while the clipboard contents have not changed
		repeat while done = "no"
			--Get the contents of the clipboard
			try
				set selecTxt to the clipboard as text
			end try
			
			--See if we're done or need to wait
			if waitnum is equal to maxwaits then
				set done to "yes"
			else if selecTxt is equal to "" then
				delay waitInterval
				set waitnum to waitnum + 1
			else
				set done to "yes"
			end if
			
		end repeat
		
		if debug is true then
			try
				display dialog "Copied text: " & (the clipboard as text)
			end try
		end if
	end tell
	
	--Restore the original clipboard contents
	set the clipboard to theSpare --as record
	
	if debug is true then
		try
			display dialog "The clipboard contents have been restored to " & (the clipboard as text)
		end try
	end if
	
	--Return the highlighted text
	return selecTxt
	
end getHighlight

on countNucleotides(dnaStr)
	set astid to AppleScript's text item delimiters
	
	set AppleScript's text item delimiters to "A"
	set aCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "T"
	set tCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "G"
	set gCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "C"
	set cCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to "B"
	set bCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "D"
	set dCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "H"
	set hCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "V"
	set vCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "R"
	set rCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "Y"
	set yCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "K"
	set kCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "M"
	set mCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "S"
	set sCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "W"
	set wCount to (count dnaStr's text items) - 1
	
	set AppleScript's text item delimiters to "N"
	set nCount to (count dnaStr's text items) - 1
	
	
	
	set AppleScript's text item delimiters to astid
	
	
	set seqTotal to aCount + tCount + gCount + cCount + bCount + dCount + hCount + vCount + rCount + yCount + kCount + mCount + sCount + wCount + nCount
	
	return (seqTotal as integer)
end countNucleotides

--Uses the down arrow to grab at least n characters of nucleotides and returns the newly selected string and the number of nucleotides it contains
on selectAtLeast(initial_str as string, n as integer, debug)
	
	set cur_str to initial_str
	set character_count to ((count characters of cur_str) as integer)
	set last_character_count to 0
	set nt_count to ((my countNucleotides(cur_str)) as integer)
	repeat while character_count > last_character_count and nt_count < n
		--Add a line to the selection
		tell application "System Events" to key code 125 using {shift down}
		set cur_str to (my getHighlight(debug))
		set last_character_count to character_count
		set character_count to ((count characters of cur_str) as integer)
		set nt_count to (my countNucleotides(cur_str))
	end repeat
	if nt_count < n then
		display dialog "Error: Unable to select enough sequence. Please make sure to select more sequence than the target length (" & (n as string) & ")."
		return ({"", 0})
	end if
	return ({cur_str as string, nt_count as integer})
end selectAtLeast

Select N Sequence Characters.scpt

--Installation: Create an Automator service, paste this code into a "Run AppleScript" action, and save.
--How to use it: 1. Copy a number indicating the length you want the selection to be. 2. Select the region of text where you want the copied length to be selected. 3. Right-click the selection and select this service.

--NOTES:
--If the contents of the clipboard is not a number, you'll be prompted to enter a length.
--If the selected text is in Terminal.app, the modified selection will display in a dialog window (because the arrow keys are used for the selection modification and that doesn't work in Terminal).  Also, if the target selection length is longer than the current selection, an error about selection length will be displayed.
--If input is not supplied, this script will backup the current clipboard, copy the current selection to get the currently selected text, then restore the clipboard.

on run {input, parameters}
	
	try
		set debug to false
		if input's class is not list then
			set input to (my getHighlight(debug))
		end if
		
		tell application "System Events"
			--See if the clipboard has a number in it to use for the selection length
			set checkClipboard to the clipboard as text
			if my isNumString(checkClipboard) then
				set n to checkClipboard as integer
			else
				--Get the name of the frontmost application so we can bring the front window back into focus after the dialog window goes away (which surprisingly, is not the default behavior)
				set curProc to (name of first process whose frontmost is true)
				
				set n to my getintvalue()
				
				--And this is the only trick I've found to bring any window in an app back into focus
				do shell script "open -a '" & (curProc as string) & "'"
				delay 0.2
			end if
			
			set {selText, nt_count} to (my selectAtLeastAln((input as string), (n as integer), debug))
			
			--Exit if an empty string was returned (indicating an error)
			if selText is "" then
				return
			end if
			
			--Estimate/guess whether it will be quicker to shrink the selection from the end or grow the selection from the beginning
			set shrinkit to ((nt_count - n) < n)
			
			--Figure out whether the selection must be lengthened or shrunk
			if nt_count is equal to 0 or n is greater than nt_count then
				display dialog "The selection length must be greater than the number of characters to select"
				return
			end if
			
			--See if we're in Terminal
			set isTerminal to ((name of first process where it is frontmost) as string) is equal to "Terminal"
			
			if isTerminal is true then
				ignoring application responses
					display dialog "Length " & n & " is selected below:" default answer selText buttons {"OK"} default button 1 with title "Selected Character Position"
				end ignoring
			end if
			
			if shrinkit is false then
				key code 123
				set str_pos to 1
				set nt_count to 0
				repeat while nt_count < n
					key code 124 using {shift down}
					set nt to text str_pos thru str_pos of selText
					if (my countSequenceChars(nt)) > 0 then
						set nt_count to nt_count + 1
					end if
					set str_pos to str_pos + 1
				end repeat
			else
				--Trick to make sure arrow presses affect the right side of the selection instead of the left
				set character_count to count characters of selText
				key code 124 using {shift down}
				key code 123 using {shift down}
				if (count characters of selText) < character_count then
					key code 124 using {shift down}
				end if
				
				set str_pos to character_count
				set nt to text str_pos thru str_pos of selText
				repeat while nt_count > n or (my countSequenceChars(nt)) < 1
					key code 123 using {shift down}
					if (my countSequenceChars(nt)) > 0 then
						set nt_count to nt_count - 1
					end if
					set str_pos to str_pos - 1
					set nt to text str_pos thru str_pos of selText
				end repeat
			end if
			delay 1
		end tell
	on error errstr
		display dialog errstr
	end try
	
end run



property mytitle : "Length of text to select"

-- I am asking the user to provide an integer
-- In case the user cancels the dialog, I return «missing value»
on getintvalue()
	set dlgmsg to "How many characters would you like to select?:"
	try
		display dialog dlgmsg default answer "1" buttons {"Cancel", "Enter"} default button 2 with title mytitle
	on error
		-- User canceled
		return missing value
	end try
	set dlgresult to result
	set usrinput to text returned of dlgresult
	-- the user did not enter anything...
	if usrinput is "" then
		my getintvalue()
	else
		-- let's check if the user entered numbers only
		set nums to {"1", "2", "3", "4", "5", "6", "7", "8", "9", "0"}
		set invalidchars to ""
		repeat with char in usrinput
			if char is not in nums then
				set invalidchars to invalidchars & char & space
			end if
		end repeat
		-- we found invalid characters
		if invalidchars is not "" then
			set errmsg to "We found the following characters in the given input. Please enter numbers only." & return & return & invalidchars & return
			my dsperrmsg(errmsg, "--")
			my getintvalue()
		else
			-- let's try to transform the user input into an integer
			try
				set intvalue to usrinput as integer
				return intvalue
			on error
				set errmsg to "We could not coerce the given input into an integer:" & return & return & usrinput & return
				my dsperrmsg(errmsg, "--")
				my getintvalue()
			end try
		end if
	end if
end getintvalue

-- I am displaying error messages to the user
on dsperrmsg(errmsg, errnum)
	tell me
		activate
		display dialog errmsg & " (" & errnum & ")" buttons {"OK"} default button 1 with title mytitle with icon stop
	end tell
end dsperrmsg

-- isNumString :: String -> Bool
on isNumString(s)
	try
		if class of s is string then
			set c to class of (s as number)
			c is real or c is integer
		else
			false
		end if
	on error
		false
	end try
end isNumString

on getHighlight(debug)
	
	--Save the current contents of the clipboard
	try
		set theSpare to the clipboard --as text
	on error
		set response to (display dialog "Warning: The contents of the clipboard will be lost." buttons {"Cancel", "OK"})
		if button returned of response is "OK" then
			set theSpare to ""
		end if
	end try
	set the clipboard to ""
	--Declare the variable we're going to return
	set selecTxt to ""
	
	tell application "System Events"
		--Initiate the copy
		keystroke "c" using {command down}
		
		--Wait up to 2 seconds for the copy to finish
		set done to "no"
		set waitnum to 0
		set waitInterval to 0.02
		set maxwaits to 100
		
		--Repeat while the clipboard contents have not changed
		repeat while done = "no"
			--Get the contents of the clipboard
			try
				set selecTxt to the clipboard as text
			end try
			
			--See if we're done or need to wait
			if waitnum is equal to maxwaits then
				set done to "yes"
			else if selecTxt is equal to "" then
				delay waitInterval
				set waitnum to waitnum + 1
			else
				set done to "yes"
			end if
			
		end repeat
		
		if debug is true then
			try
				display dialog "Copied text: " & (the clipboard as text)
			end try
		end if
	end tell
	
	--Restore the original clipboard contents
	set the clipboard to theSpare --as record
	
	if debug is true then
		try
			display dialog "The clipboard contents have been restored to " & (the clipboard as text)
		end try
	end if
	
	--Return the highlighted text
	return selecTxt
	
end getHighlight

on countSequenceChars(seq)
	set AppleScript's text item delimiters to {space, tab, linefeed, return}
	set selText to text items of seq
	set AppleScript's text item delimiters to {}
	set selText to selText as string
	
	set len to count characters of selText
	
	
	return (len as integer)
end countSequenceChars

--Uses the down arrow to grab at least n characters of nucleotides and returns the newly selected string and the number of nucleotides it contains
on selectAtLeastAln(initial_str as string, n as integer, debug)
	
	set cur_str to initial_str
	set character_count to ((count characters of cur_str) as integer)
	set last_character_count to 0
	set nt_count to ((my countSequenceChars(cur_str)) as integer)
	repeat while character_count > last_character_count and nt_count < n
		--Add a line to the selection
		tell application "System Events" to key code 125 using {shift down}
		set cur_str to (my getHighlight(debug))
		set last_character_count to character_count
		set character_count to ((count characters of cur_str) as integer)
		set nt_count to (my countSequenceChars(cur_str))
	end repeat
	if nt_count < n then
		display dialog "Error: Unable to select enough sequence. Please make sure to select more sequence than the target length (" & (n as string) & ")."
		return ({"", 0})
	end if
	return ({cur_str as string, nt_count as integer})
end selectAtLeastAln