From 6cabd2496244ebe739aeb7e0237ac52cb62d7442 Mon Sep 17 00:00:00 2001
From: luissian <chapado.l@gmail.com>
Date: Thu, 25 Jan 2024 17:27:04 +0100
Subject: [PATCH] fixing liting and update test

---
 .github/workflows/tests.yml | 4 ++--
 taranis/__main__.py         | 5 ++---
 taranis/analyze_schema.py   | 8 +++++---
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 9a8095c..d8bb01c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -28,6 +28,6 @@ jobs:
           conda activate taranis_env
       - name: testung analyze schema
         run:
-          pip install .
-          taranis analyze-schema -i  test/MLST_listeria -o analyze_schema_test  --cpus 1
+          poetry install
+          taranis analyze-schema -i  test/MLST_listeria -o analyze_schema_test  --cpus 1 --output-allele-annot --remove-no-cds --remove-duplicated --remove-subset
           
\ No newline at end of file
diff --git a/taranis/__main__.py b/taranis/__main__.py
index da1ed40..6243bba 100644
--- a/taranis/__main__.py
+++ b/taranis/__main__.py
@@ -90,6 +90,7 @@ def decorator(f):
             cmd = super(CustomHelpOrder, self).command(*args, **kwargs)(f)
             help_priorities[cmd.name] = help_priority
             return cmd
+
         return decorator
 
 
@@ -120,6 +121,7 @@ def taranis_cli(verbose, log_file):
         )
         log.addHandler(log_fh)
 
+
 @taranis_cli.command(help_priority=1)
 @click.option(
     "-i",
@@ -223,8 +225,6 @@ def analyze_schema(
             results.append(future.result())
     _ = taranis.analyze_schema.collect_statistics(results, output, output_allele_annot)
 
-    _ = taranis.analyze_schema.collect_statistics(schema_analyze, output, output_allele_annot)
-
     finish = time.perf_counter()
     print(f"Schema analyze finish in {round((finish-start)/60, 2)} minutes")
 
@@ -251,7 +251,6 @@ def reference_alleles(
     schema: str,
     output: str,
 ):
-
     schema_files = taranis.utils.get_files_in_folder(schema, "fasta")
 
     # Check if output folder exists
diff --git a/taranis/analyze_schema.py b/taranis/analyze_schema.py
index 4977a43..6cb4206 100644
--- a/taranis/analyze_schema.py
+++ b/taranis/analyze_schema.py
@@ -152,7 +152,9 @@ def check_allele_quality(self, prokka_annotation: dict) -> OrderedDict:
             try:
                 unique_seq.remove(seq_value)
             except ValueError:
-                log.warning("Already  deleted same sequence as for record id  %s" , record.id)
+                log.warning(
+                    "Already  deleted same sequence as for record id  %s", record.id
+                )
             if seq_value in unique_seq:
                 a_quality[rec_id]["quality"] = "Bad quality"
                 a_quality[rec_id]["reason"] = "Sub set allele"
@@ -295,8 +297,8 @@ def stats_graphics(stats_folder: str) -> None:
 
         # create graphic for alleles/number of genes
         group_alleles_df = stats_df.groupby(
-                pd.cut(stats_df["num_alleles"], allele_range)
-            ).count()
+            pd.cut(stats_df["num_alleles"], allele_range)
+        ).count()
         _ = taranis.utils.create_graphic(
             graphic_folder,
             "num_genes_per_allele.png",