Remove unnecessary 'multi' parameter from Prodigal command in PLAST class

k-krakowski · k-krakowski · commit f08cf386420e · 2025-11-26T19:56:49.000+01:00
diff --git a/plast/plast.py b/plast/plast.py
@@ -386,7 +386,7 @@ def load_nt_fasta(self, input_fasta: Union[str, any]) -> "PLAST":
                 cmd = (
                     f"{prodigal} -i {input_file.name}"
                     f" -a {output_file.name}"
-                    f" -g 11 -p multi -q"
+                    f" -g 11 -q"
                 )
                 if self.length < 100000:
                     cmd += " -p meta"

Original file line number	Diff line number	Diff line change
`@@ -386,7 +386,7 @@ def load_nt_fasta(self, input_fasta: Union[str, any]) -> "PLAST":`
`386`	`386`	`cmd = (`
`387`	`387`	`f"{prodigal} -i {input_file.name}"`
`388`	`388`	`f" -a {output_file.name}"`
`389`		`- f" -g 11 -p multi -q"`
	`389`	`+ f" -g 11 -q"`
`390`	`390`	`)`
`391`	`391`	`if self.length < 100000:`
`392`	`392`	`cmd += " -p meta"`