From 2e9cc49fee997cfd4aebd5cb9797661350cb75b5 Mon Sep 17 00:00:00 2001 From: Chunyu Ma Date: Fri, 23 Feb 2024 12:17:41 -0500 Subject: [PATCH 1/3] fix a bug reported in issue #114 --- yacht/standardize_yacht_output.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/yacht/standardize_yacht_output.py b/yacht/standardize_yacht_output.py index 02c7e20..9b73bff 100644 --- a/yacht/standardize_yacht_output.py +++ b/yacht/standardize_yacht_output.py @@ -248,8 +248,8 @@ def __to_cami(self, sample_name): ## select the organisms that YACHT considers to present in the sample yacht_res_df = self.yacht_output.copy() - organism_name_list = yacht_res_df["organism_name"].tolist() - organism_id_list = [x.split(" ")[0] for x in organism_name_list] + organism_id_list = yacht_res_df["organism_name"].tolist() + # organism_id_list = [x.split(" ")[0] for x in organism_name_list] if len(organism_id_list) == 0: logger.error("No organism is detected by YACHT.") From f4e7825299390728b01549dcb57c0e52c656b786 Mon Sep 17 00:00:00 2001 From: Chunyu Ma Date: Fri, 23 Feb 2024 12:18:49 -0500 Subject: [PATCH 2/3] update version to 1.2.2 for the recent bug fixes --- yacht/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/yacht/utils.py b/yacht/utils.py index 9c6da58..9757eba 100644 --- a/yacht/utils.py +++ b/yacht/utils.py @@ -19,7 +19,7 @@ COL_NOT_FOUND_ERROR = "Column not found: {}" # Set up global variables -__version__ = "1.2.1" +__version__ = "1.2.2" GITHUB_API_URL = "https://api.github.com/repos/KoslickiLab/YACHT/contents/demo/{path}" GITHUB_RAW_URL = "https://raw.githubusercontent.com/KoslickiLab/YACHT/main/demo/{path}" BASE_URL = "https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/" From 9dbfc797a1002accb7990c4faa4d343f2bc00594 Mon Sep 17 00:00:00 2001 From: Chunyu Ma Date: Fri, 23 Feb 2024 12:24:03 -0500 Subject: [PATCH 3/3] fixed an issue reported by SonarCloud Code Analysis --- yacht/standardize_yacht_output.py | 1 - 1 file changed, 1 deletion(-) diff --git a/yacht/standardize_yacht_output.py b/yacht/standardize_yacht_output.py index 9b73bff..f168c38 100644 --- a/yacht/standardize_yacht_output.py +++ b/yacht/standardize_yacht_output.py @@ -249,7 +249,6 @@ def __to_cami(self, sample_name): ## select the organisms that YACHT considers to present in the sample yacht_res_df = self.yacht_output.copy() organism_id_list = yacht_res_df["organism_name"].tolist() - # organism_id_list = [x.split(" ")[0] for x in organism_name_list] if len(organism_id_list) == 0: logger.error("No organism is detected by YACHT.")