Why use Genbank's type for your feature name? about alignparse HOT 2 CLOSED

Yes that does make sense. Hand annotation is annoying adding the qualifiers.

I just now thought about subclassing Target to change that __init__ behavior. That alone may allow my script to be usable. And would not require any trouble on your part. I will have to see.

At this point, we don't want to change it entirely to avoid breaking backward-compatibility with what we've already done.

Yes I can see this as well, but the subclassing solution may make this moot.

However, I think it would be possible to pretty easily add few lines of code to the init method of Targets that adds a parameter that specifies if the name is read from the feature type (as currently) or some other Genbank field given by that parameter.

Yes I was also thinking of this as a solution that would default to the old behavior but allow for adjustment.

Are you interested in making a pull request to do this?

I think that I could do this pretty easily, and would be honored to contribute. I will start playing.

Alternatively, if you want to post an example of a Genbank for which you'd like to parse a different field (e.g., name), then I can try to do this at some point soon.

If need be I can post something but I think that you have given me enough here to get traction on the problem. Thank you.

I will take a look and submit a PR if I am able to get it to work.

Thanks again for this library.

from alignparse.

Yes, I agree with your comment and understand why this could be problematic.

We originally designed this way as we were initially mostly "hand-annotating" Genbank maps and it is easier to set the type of a feature than the names as I had a hard time understanding exactly how those were standardly specified in a Genbank file. But I agree this creates the problem you mention.

At this point, we don't want to change it entirely to avoid breaking backward-compatibility with what we've already done.

However, I think it would be possible to pretty easily add few lines of code to the __init__ method of Targets that adds a parameter that specifies if the name is read from the feature type (as currently) or some other Genbank field given by that parameter.

Are you interested in making a pull request to do this? Alternatively, if you want to post an example of a Genbank for which you'd like to parse a different field (e.g., name), then I can try to do this at some point soon.

from alignparse.