Scripting in CodonCode Aligner 2.0.6

[bbimber]

I am trying to script some basic sequence processing tasks. I would like the end-product of the script to be an aligner project, which is why I am trying to use aligner, not phred/phrap.

Most commands seem straightforward, however I have a couple questions:

With all assembly commands, can i specify paramters like 'min percent match' within the script or will these always use the aligner defaults?

Can I trim vector using a script? Can i specify the trim vector within the script?

Can I execute the 'change bases' command from a script? Can i set the minimum Q-score within the script or is this limited to the aligner default?

Thank you for any help.

[Peter Richterich]

With all assembly commands, can i specify parameters like 'min percent match' within the script or will these always use the aligner defaults?
Can I trim vector using a script? Can i specify the trim vector within the script?
Can I execute the 'change bases' command from a script? Can i set the minimum Q-score within the script or is this limited to the aligner default?

You cannot do any of these things in CodonCode Aligner version 2.0.6. We have added these as feature requests, and plan to add at least some of them to the next major release of CodonCode Aligner.