Skip to content

Commit

Permalink
Fixup some documentation bugs.
Browse files Browse the repository at this point in the history
  • Loading branch information
tfenne committed Nov 8, 2024
1 parent eb5dc15 commit b111c20
Showing 1 changed file with 2 additions and 12 deletions.
14 changes: 2 additions & 12 deletions prymer/api/picking.py
Original file line number Diff line number Diff line change
@@ -1,21 +1,11 @@
"""
# Methods and class for building and scoring primer pairs from a list of left and right primers.
Typically, the first step is to build primer pairs from a list of left and right primers for a
Typically, primer pairs are built from a list of left and right primers for a
given target with the [`build_primer_pairs()`][prymer.api.picking.build_primer_pairs]
method. The returned primer pairs are automatically scored (using the
[`score()`][prymer.api.picking.score] method).
Next, the list of primer pairs for a given target are filtered based on various criteria using the
[`pick_top_primer_pairs()`][prymer.api.picking.pick_top_primer_pairs] method. Criteria
included but not limited to filtering for desired size and melting temperature ranges (see
[`is_acceptable_primer_pair()`][prymer.api.picking.is_acceptable_primer_pair]), not too
many off-targets, no self-dimers, and so on. A given maximum number of passing primer pairs is
returned.
These two steps can be performed jointly using the
[`build_and_pick_primer_pairs()`][prymer.api.picking.build_and_pick_primer_pairs] method.
## Module contents
Contains the following public classes and methods:
Expand Down Expand Up @@ -123,7 +113,7 @@ def build_primer_pairs(
amplicon_sizes: minimum, optimal, and maximum amplicon sizes (lengths)
amplicon_tms: minimum, optimal, and maximum amplicon Tms
max_heterodimer_tm: if supplied, heterodimer Tms will be calculated for primer pairs,
and those exceeding the maximum Tm will be discarded
and those exceeding the maximum Tm will be discarded
weights: the set of penalty weights
fasta_path: the path to the FASTA file from which the amplicon sequence will be retrieved.
Expand Down

0 comments on commit b111c20

Please sign in to comment.