Skip to content
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.

Sign up for GitHub

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

ENH: adds --p-[no-]keep-primers option to trim-alignment. #214

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

ENH: adds --p-[no-]keep-primers option to trim-alignment. #214

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
2513037
initial draft to toggle the return of primers within extracted amplic…
mikerobeson Feb 3, 2025
7ac6649
minor test and parameter relabelling updates
mikerobeson Feb 3, 2025
5d6534b
fix typo
mikerobeson Feb 3, 2025
5a92467
merged with master
mikerobeson Feb 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 12 additions & 6 deletions rescript/plugin_setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1061,6 +1061,7 @@
'primer_rev': Str,
'position_start': Int % Range(1, None),
'position_end': Int % Range(1, None),
'keep_primer_location': Bool,
'n_threads': Int % Range(1, None),
},
outputs=[('trimmed_sequences', FeatureData[AlignedSequence]), ],
Expand All @@ -1078,6 +1079,11 @@
'will end. If not provided, alignment will not be '
'trimmed at the end. If reverse primer is specified '
'this parameter will be ignored.',
'keep_primer_location': 'Retain the alignment positions of the '
'primer binding location. Note: the '
'primers themselves will be removed, but '
'the alignment positions where the primers '
'align will be retained in the alignment.',
'n_threads': 'Number of threads to use for primer-based trimming, '
'otherwise ignored. (Use `auto` to automatically use '
'all available cores)'
Expand All @@ -1093,12 +1099,12 @@
"alignment will be generated to locate primer positions. "
"Subsequently, start (5'-most) and end (3'-most) position from fwd "
"and rev primer located within the new alignment is identified and "
"used for slicing the original alignment. That is, the primer region "
"will be included in the new alignment output. WARNING: finding "
"alignment positions via primer search can be inefficient for very "
"large alignments and is only recomended for small alignments. "
"For large alignments providing specific alignment positions is "
"ideal."),
"used for slicing the original alignment. The retention of alignment "
"positions that span the primer locations can be toggled. "
"WARNING: finding alignment positions via primer search can be "
"inefficient for very large alignments and is only recomended for "
"small alignments. For large alignments providing specific alignment "
"positions is ideal."),
)

T = TypeMatch([AlignedSequence, Sequence])
Expand Down
Loading
Loading