Added basic support for auto reverse-complements

[tolot27]

Added basic support for reverse-complement a sequence automatically, if the start coordinate of a range is larger than the end coordinate.

It is useful, i.e. to directly extract subsequences based on BLAST hit coordinates without dealing with its strandness.

[tolot27]

Maybe I should test strict_bounds, too?

[mdshw5]

I’d gladly accept this but would like to know if complementing the sequence is expected behavior. Can you point me to an example of coordinates working this way in another program?

[swheelan]

I think it could be a flag but not default behavior. The yeast genomics community traditionally works this way, and it would be a handy feature to have for annotations produced in that format. Also, BLAST output convention is that start > stop is assumed to be the minus strand, so I can see how it’s useful. In general, though, coordinates out of order should generate a warning.

…

On Jul 25, 2017, at 9:32 AM, Matt Shirley ***@***.***> wrote: I’d gladly accept this but would like to know if complementing the sequence is expected behavior. Can you point me to an example of coordinates working this way in another program? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#120 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFnA5F_YQzfyyr2EDvyp4GoeWoeMALzbks5sRe5dgaJpZM4OiUOn>.

[tolot27]

Not only complementing, also reversing. ;-)
A flag would be sufficient.

[mdshw5]

Thanks, @swheelan. @tolot27: I'll merge the changes and add a flag --auto-strand flag to the script.