From d4f1cff15d9ff4340a598ae51abf98584cb409c5 Mon Sep 17 00:00:00 2001 From: Michal Puncochar Date: Wed, 27 Sep 2023 23:49:20 +0200 Subject: [PATCH] Specify phylophlan params for trimming --- metaphlan/utils/phylophlan_controller.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/metaphlan/utils/phylophlan_controller.py b/metaphlan/utils/phylophlan_controller.py index 41750bd..49fb2eb 100644 --- a/metaphlan/utils/phylophlan_controller.py +++ b/metaphlan/utils/phylophlan_controller.py @@ -90,7 +90,8 @@ def execute_phylophlan(self, samples_markers_dir, tmp_dir): cmd = f'phylophlan' \ f' -i {samples_markers_dir} -o . --output_folder {self.output_dir} --nproc {self.nprocs}' \ f' --strainphlan --{self.phylophlan_mode} --data_folder {tmp_dir} -f {self.phylophlan_configuration}' \ - f' -t n --diversity low --genome_extension fna --min_num_entries 1 --min_num_markers 1' + f' -t n --diversity low --genome_extension fna --min_num_entries 1 --min_num_markers 1' \ + f' --fragmentary_threshold 1.0 --not_variant_threshold 1.0 --gap_perc_threshold 0.8' if self.phylophlan_params is not None: cmd += " " + self.phylophlan_params