From dc70dcc790ecc9827a77e94ebaf929eaf52ae5c5 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Thu, 11 Feb 2021 15:49:27 +0000 Subject: [PATCH] Change node_number to node_id for issue #1 --- polecat/scripts/polecatfunks.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/polecat/scripts/polecatfunks.py b/polecat/scripts/polecatfunks.py index 23ed1ab..4677777 100644 --- a/polecat/scripts/polecatfunks.py +++ b/polecat/scripts/polecatfunks.py @@ -30,7 +30,7 @@ def get_defaults(): "max_recency":"", "max_size":"", "min_size":"", - "stats":"node_number,day_range,growth_rate,tip_count,lineage,uk_lineage", + "stats":"node_id,day_range,growth_rate,tip_count,lineage,uk_lineage", "background_fields":"sequence_name,sample_date,epi_week,country,adm2,uk_lineage,lineage,phylotype", "command":"", "min_UK":"", @@ -50,8 +50,8 @@ def get_defaults(): "config":False, "data_column":"sequence_name", "output_prefix":"polecat", - "summary_fields":"node_number,most_recent_tip,tip_count,admin0_count,admin1_count", - "cluster_fields":"node_number,day_range,tip_count,uk_tip_count,uk_chain_count,identical_count", + "summary_fields":"node_id,most_recent_tip,tip_count,admin0_count,admin1_count", + "cluster_fields":"node_id,day_range,tip_count,uk_tip_count,uk_chain_count,identical_count", "no_temp":False, "force":True, "launch_browser":False, @@ -216,7 +216,7 @@ def report_group_to_config(args,config): def get_stat_list(): - return "node_number,parent_number,most_recent_tip,least_recent_tip,day_range,persistence,recency,age,tip_count,uk_tip_count,uk_child_count,uk_chain_count,identical_count,divergence_ratio,mean_tip_divergence,stem_length,growth_rate,lineage,uk_lineage,proportion_uk,admin0_count,admin1_count,admin2_count,admin0_mode,admin1_mode,admin2_mode,admin1_entropy,admin2_entropy,tips".split(",") + return "node_id,parent_id,most_recent_tip,least_recent_tip,day_range,persistence,recency,age,tip_count,uk_tip_count,uk_child_count,uk_chain_count,identical_count,divergence_ratio,mean_tip_divergence,stem_length,growth_rate,lineage,uk_lineage,proportion_uk,admin0_count,admin1_count,admin2_count,admin0_mode,admin1_mode,admin2_mode,admin1_entropy,admin2_entropy,tips".split(",") def check_metadata_for_stat_fields(config):