Using Applescript to batch convert files.

Up until MacVector 13 Applescript support was fairly limited. However, with this release we’ve started to expand it. The first enhancement has been to improve the export of files. Now you can export files to any supported format. Over the next few releases this support will be further expanded to include some analysis tools. If a particular tool would be helpful for you please do let us know.

There’s an Applescript folder in the MacVector Application folder. This contains two very simple scripts to use to build your own.

One of the scripts will batch convert a folder of sequences into Genbank format. Here’s a modified version of that script with these changes:

The script is too long to place here but the relevant MacVector part of the code is here:

	if mvExtension = "nucl" then
		tell application "MacVector"
			--Now open the file
			open f
			delay 0.3 -- wait a little bit until MV has opened the file
			--now save it as a genbank file
			set docRef to (a reference to the first document)
			if SeqFormat = "fasta" then
				save docRef in outputFilePath as FASTA
			else
				save docRef in outputFilePath as GenBank
			end if
			close docRef
		end tell
		

Download the full script here.

Many thanks to Chris Buck for all his invaluable feedback on this script.

If you have any useful scripts please let us know.