-
Notifications
You must be signed in to change notification settings - Fork 21
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Adds --keeplength
flag to maff-add action.
#84
Conversation
Hey @mikerobeson! It looks like some of the tests are now failing, should keeplength in the |
@@ -26,7 +26,8 @@ def run_command(cmd, output_fp, verbose=True): | |||
subprocess.run(cmd, stdout=output_f, check=True) | |||
|
|||
|
|||
def _mafft(sequences_fp, alignment_fp, n_threads, parttree, addfragments): | |||
def _mafft(sequences_fp, alignment_fp, n_threads, parttree, addfragments, | |||
keeplength): |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
keeplength): | |
keeplength=False): |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I left this as is for now as it is similar to addfragments
. I just I just followed that lead of adding False
in the mafft
function. I can change that it that is the better way to go. :-)
@ebolyen, looks like the check pass now. :-) |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Looks good @mikerobeson!
Resolves #83
Allows an option to force the original alignment to keep it's original length while adding new sequences, as outlined here.
Users should keep in mind the following from the mafft docs (which is also in the plugin help text):