Set myFile to open for access (outputFolder & "All_CDS.fasta") with write permission " & theTranslation - includes two new lines as \n but ScriptEditor always expands these. Set outputCount to outputCount + 1 - increment the number of CDS translated Set theName to the theFeature's key as text
Repeat with theFeature in (every feature of theSequence whose key is "CDS") With timeout of 10000 seconds - add very long timeout to avoid timeouts when translating long sequences. Set OutputFilename to text returned of result Set defaultAnswer to "All_CDS_translated.fa"ĭisplay dialog "Please enter the Output filename:" default answer defaultAnswer Use AppleScript version "2.7" - macOS High Sierra or later added direct writing of output fasta file
#Macvector transloation full
The full script is here: - Translate all CDS features in a MacVector Nucl sequence Set theTranslation to theFeature's translation as textĪll they do is tell MacVector to look for a CDS feature and then translate that open reading frame. The important lines are these two: repeat with theFeature in (every feature of theSequence whose key is "CDS") If your sequence does not have any CDS features, then you can use SCAN FOR…ORFS to easily add them. Incidentally many tools in MacVector rely on annotated CDS features. Finally producing a FASTA sequence containing every protein sequence. Once a CDS feature was found it is translated, then onto the next CDS feature and so on. The simple workflow for the script is to go through a DNA sequence and look for every CDS feature. However, with AppleScript once a script has been written it is a simple task. Whereas MacVector can easily translate single CDS features or do a six frame translation of a sequence, repeating this for a large genome with multiple ORFs would be laborious to do manually. This is a task very well suited to automation. Recently we had a support query about translating all the open reading frames in a single sequence to a set of protein sequences. Even mundane tasks such as converting a folder of sequences into a different format. AppleScript is excellent for any task that requires any batch operations, whether a single operation on multiple input sequences, multiple operations on a single sequence, or taking a single sequence and producing multiple results.
You can auto annotate multiple sequences, search for sequences in Entrez and retrieve them, Translate sequences, Transcribe sequences and more. MacVector has many such functions in its AppleScript Dictionary. Many Apple applications have a AppleScript Dictionary that defines what functions you can automate. Apple’s AppleScript (along with Javascript for Automation) is an easy to write and easy to understand language that allows you to easily automate tasks in supported applications.
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