Target - strand features

[greenkidneybean]

This is a long shot, but could the Target class include - strand features? My pacbio_amplicon.gb includes a single barcode and two genes in reverse orientations. My work-around is to run the pipeline twice with each gene on the + strand, then merge outputs on the barcodes.

file: alignparse/targets.py
lines: 162-166

            if bio_feature.location.strand != 1:
                raise ValueError(
                    f"feature {feature_name} of {self.name} is - "
                    "strand, but only + strand features handled"
                )

[jbloom]

This functionality should be possible in principle, but in reality I doubt I will have time to figure out how to implement this in the near future...

So for now, running two ways like you are doing may be the best bet.

It would also be great if you decide you want to tackle a pull request to make the change.

Alternatively, I will keep this issue open and hopefully get to it eventually, but don't anticipate being able to do that in a short timeframe.

[greenkidneybean]

Thanks Jesse! Feel free to close this issue, no need to turn it into a time suck. I'll follow-up with a pull request if I get something working. Cheers!