Skip to content

Commit

Permalink
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Edit help text
Browse files Browse the repository at this point in the history
huddlej committed Aug 21, 2024
1 parent 92e3ce0 commit b188bda
Showing 1 changed file with 8 additions and 1 deletion.
9 changes: 8 additions & 1 deletion src/pathogen_embed/__main__.py
Original file line number Diff line number Diff line change
@@ -103,7 +103,14 @@ def make_parser_cluster():
return parser

def make_parser_cluster_mutations():
parser = argparse.ArgumentParser(description = "find mutations associated with clusters", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = argparse.ArgumentParser(
description="""Find mutations associated with clusters.
First, find pairwise mutations between each sequence in the given alignment and the given reference.
Then, filter to mutations that are present in at least a fixed number or proportion of sequences in cluster.
Finally, output a table of mutations as '<position><allele>' with the number and list of clusters each mutation appears in.
""",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)

parser.add_argument("--reference-sequence", required=True, help="FASTA file of the reference sequence used for the alignment")
parser.add_argument("--alignment", required=True, help="a FASTA file of an alignment used to create clusters")

0 comments on commit b188bda

Please sign in to comment.