V0.4.1

.github/workflows/ci.yml

@@ -0,0 +1,40 @@
+name: StaphSCAN test
+
+on:
+  push:
+    branches: [ "main", "master" ]
+  pull_request:
+    branches: [ "main", "master" ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+
+    - name: Install Mash and blast
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y mash ncbi-blast+
+
+    - name: Install dependencies and staphscan
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pandas
+        pip install . 
+
+    - name: Run full pipeline test
+      run: |
+        pytest test/ -v

CHANGELOG.md

@@ -0,0 +1,92 @@
+# Changelog
+
+## [Unreleased](https://github.com/riccabolla/staphscan/tree/HEAD)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.4.0...HEAD)
+
+**Implemented enhancements:**
+
+- v0.4.0 release [\#13](https://github.com/riccabolla/StaphSCAN/issues/13)
+
+## [v0.4.0](https://github.com/riccabolla/staphscan/tree/v0.4.0) (2026-06-26)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.3.1...v0.4.0)
+
+**Fixed bugs:**
+
+- error in containers built from Bioconda [\#11](https://github.com/riccabolla/StaphSCAN/issues/11)
+
+**Merged pull requests:**
+
+- V0.4.0 [\#14](https://github.com/riccabolla/StaphSCAN/pull/14) ([riccabolla](https://github.com/riccabolla))
+
+## [v0.3.1](https://github.com/riccabolla/staphscan/tree/v0.3.1) (2026-05-02)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.3.0...v0.3.1)
+
+**Implemented enhancements:**
+
+- mlst downgrade [\#10](https://github.com/riccabolla/StaphSCAN/issues/10)
+
+**Merged pull requests:**
+
+- V0.3.1 [\#12](https://github.com/riccabolla/StaphSCAN/pull/12) ([riccabolla](https://github.com/riccabolla))
+
+## [v0.3.0](https://github.com/riccabolla/staphscan/tree/v0.3.0) (2026-03-23)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.2.1...v0.3.0)
+
+**Closed issues:**
+
+- Broken DOI badge [\#9](https://github.com/riccabolla/StaphSCAN/issues/9)
+
+## [v0.2.1](https://github.com/riccabolla/staphscan/tree/v0.2.1) (2026-03-06)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.2.0...v0.2.1)
+
+**Fixed bugs:**
+
+- Error running resistance: sequence has zero length [\#8](https://github.com/riccabolla/StaphSCAN/issues/8)
+
+## [v0.2.0](https://github.com/riccabolla/staphscan/tree/v0.2.0) (2026-02-26)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.1.3...v0.2.0)
+
+**Fixed bugs:**
+
+- sccmec subtype [\#7](https://github.com/riccabolla/StaphSCAN/issues/7)
+
+## [v0.1.3](https://github.com/riccabolla/staphscan/tree/v0.1.3) (2026-02-16)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.1.2...v0.1.3)
+
+## [v0.1.2](https://github.com/riccabolla/staphscan/tree/v0.1.2) (2026-02-08)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.1.1...v0.1.2)
+
+## [v0.1.1](https://github.com/riccabolla/staphscan/tree/v0.1.1) (2026-02-03)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/v0.1.0...v0.1.1)
+
+**Closed issues:**
+
+- First release issues [\#2](https://github.com/riccabolla/StaphSCAN/issues/2)
+
+## [v0.1.0](https://github.com/riccabolla/staphscan/tree/v0.1.0) (2026-02-02)
+
+[Full Changelog](https://github.com/riccabolla/staphscan/compare/d72545e6a8e370300f26ccf4d23eb2a329cd199d...v0.1.0)
+
+**Implemented enhancements:**
+
+- Res db [\#5](https://github.com/riccabolla/StaphSCAN/issues/5)
+- mlst [\#4](https://github.com/riccabolla/StaphSCAN/issues/4)
+- biofilm submodule [\#3](https://github.com/riccabolla/StaphSCAN/issues/3)
+- Output [\#1](https://github.com/riccabolla/StaphSCAN/issues/1)
+
+**Closed issues:**
+
+- Complete report [\#6](https://github.com/riccabolla/StaphSCAN/issues/6)
+
+
+
+\* *This Changelog was automatically generated by [github_changelog_generator](https://github.com/github-changelog-generator/github-changelog-generator)*

README.md

@@ -1,4 +1,5 @@
 # StaphSCAN
+[![CI](https://github.com/riccabolla/staphscan/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/riccabolla/staphscan/actions/workflows/ci.yml)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/staphscan/badges/version.svg)](https://anaconda.org/bioconda/staphscan)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/staphscan/badges/latest_release_date.svg)](https://anaconda.org/bioconda/staphscan)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/staphscan/badges/license.svg)](https://anaconda.org/bioconda/staphscan)

docs/assembly.md

@@ -38,6 +38,7 @@ To report the species, the following criteria are used:
 For assembly quality the following parameters are considered:
 
 * Total assembly size (compared to expected size for *Staphylococcus aureus* of 2.6 - 3.1 Mbp)
+* Contamination: If more than one reference genome returns a Mash distance of **≤ 0.04**, the assembly is flagged (`Mixed`). This indicates an intra-genus mixed culture (e.g., *S. aureus* + *S. epidermidis*).
 * N50 (>=10 kbp)
 * Presence of ambiguous bases (Ns)
 
@@ -48,7 +49,10 @@ The assembly module generates the following output columns in the report:
 |Field|Description|
 |-----|-----------|
 |`Species`|Detected specie|
+|`Mash_distance`|Calculated Mash distance to the best-matching reference genome|
 |`Total_size`|Assembly size (bp)|
+|`N_contig`|Total number of contigs in the assembly|
+|`N50`|Assembly N50 value|
 |`QC`|Overall QC status (`PASS`  or `FAILED`)|
 
 

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="staphscan",
-    version="0.4.0",  
+    version="0.4.1",  
     description="A tool for Staphylococcus aureus analysis",
     author="Riccardo Bollini",  
     url="https://github.com/riccabolla/StaphSCAN", 

staphscan/main.py

@@ -181,7 +181,9 @@ def main():
     df = pd.DataFrame(all_results).fillna("-")
 
     summary_cols = [
-        "Sample", "Species", "Total_size", "QC", "ST", "arcC", "aroE", "glpF", "gmk", "pta", "tpi", "yqiL", "spa_type", #assembly module
+        "Sample", "Species", "Mash_distance","Total_size", "N_contig", "N50", "QC", #assembly module
+        "ST", "arcC", "aroE", "glpF", "gmk", "pta", "tpi", "yqiL", # st module
+        "spa_type", # spa module
         "cap_type", "cap_completeness", "cap_genes", #capsule module
         "sccmec_type", "sccmec_subtype", "sccmec_genes", #sccmec module
         "agr_type", "agr_confidence", "agr_frameshifts", "agr_operon_status", #agr module

staphscan/modules/assembly/assembly.py

@@ -15,19 +15,35 @@ def __init__(self):
 
     def check_db(self):
         if not self.db_sketch.exists():
-            print("Warning: Mash sketch 'staph_refs.msh' not found. Run setup_mash.py.")
+            print(f"Warning: Mash sketch '{self.db_sketch.name}' not found. Skipping assembly module.")
             return False
         return True
 
     def run(self, assembly_path):
-        contig_count, n50, longest, total_size, ambig = self.get_contig_stats(assembly_path)
-        species_call, mash_dist = self.run_mash(assembly_path)
+        # if db is missing skip and report na results
+        if not self.check_db():
+            return {
+                "Species": "Not Analyzed",
+                "Mash_distance": "-",
+                "Total_size": "-",
+                "QC": "SKIPPED (Missing DB)",
+                "N_contig": "-",
+                "N50": "-"
+            }
+        contig_count, n50, total_size, ambig = self.get_contig_stats(assembly_path)
+
+        species_call, mash_dist, is_mixed = self.run_mash(assembly_path)
+
         qc_failures = []
         if total_size < self.min_size: qc_failures.append("Too short")
         if total_size > self.max_size: qc_failures.append("Too long")
         if n50 < self.min_n50: qc_failures.append("Low_N50")
         if "yes" in ambig: qc_failures.append("Ambiguous_Bases")
 
+        # Add contamination QC checks
+        if is_mixed: qc_failures.append("Mixed")
+        #if is_weak: qc_failures.append("Weak hit")
+
         qc_status = "PASS"
         if qc_failures:
             qc_status = f"FAILED ({','.join(qc_failures)})"
@@ -37,55 +53,54 @@ def run(self, assembly_path):
             "Mash_distance": mash_dist,
             "Total_size": total_size,
             "QC": qc_status,
-            "contig_count": contig_count,
-            "N50": n50,
-            "largest_contig": longest,
-            "ambiguous_bases": ambig
+            "N_contig": contig_count,
+            "N50": n50
         }
 
     def run_mash(self, assembly_path):
         try:
             cmd = ["mash", "dist", str(self.db_sketch), str(assembly_path)]
             res = subprocess.run(cmd, capture_output=True, text=True)
-            if not res.stdout: return "Unknown", "-"
+            if not res.stdout: return "Unknown", "-", False
+
             rows = []
             for line in res.stdout.strip().split('\n'):
                 parts = line.split('\t')
                 ref_name = Path(parts[0]).name 
                 dist = float(parts[2])
                 rows.append((ref_name, dist))
+
             rows.sort(key=lambda x: x[1])
             best_match = rows[0]
             best_name = best_match[0]
             best_dist = best_match[1]
-            display_name = "Unknown"
-            if "S_aureus" in best_name: display_name = "S. aureus"
-            elif "S_epidermidis" in best_name: display_name = "S. epidermidis"
-            elif "S_lugdunensis" in best_name: display_name = "S. lugdunensis"
-            elif "S_haemolyticus" in best_name: display_name = "S. haemolyticus"
-            elif "S_argenteus" in best_name: display_name = "S. argenteus"
-            elif "S_capitis" in best_name: display_name = "S. capitis"
-            elif "S_schweitzeri" in best_name: display_name = "S. schweitzeri"
-            else: display_name = best_name
-            # if best_dist <= 0.02:
-            #     if display_name == "S. aureus":
-            #         return "S. aureus (Strong match)", str(best_dist)
-            #     else:
-            #         return display_name, str(best_dist)
-            # elif best_dist <= 0.04:
-            #     if display_name == "S. aureus":
-            #         return "S. aureus (Weak match)", str(best_dist)
-            #     else:
-            #         return display_name, str(best_dist)
-            # else:
-            #     return "No match found", str(best_dist)
+
+            # Contamination Logic: Check if multiple species are under 0.04 distance
+            close_matches = [r for r in rows if r[1] <= 0.04]
+            is_mixed = len(close_matches) > 1
+
+            # weak hits between 0.02 and 0.04
+            #is_weak = 0.02 < best_dist <= 0.04
+
+            species_map = {
+                "S_aureus": "S. aureus",
+                "S_epidermidis": "S. epidermidis",
+                "S_lugdunensis": "S. lugdunensis",
+                "S_haemolyticus": "S. haemolyticus",
+                "S_argenteus": "S. argenteus",
+                "S_capitis": "S. capitis",
+                "S_schweitzeri": "S. schweitzeri"
+            }
+
+            display_name = next((v for k, v in species_map.items() if k in best_name), best_name)
+
             if best_dist <= 0.04:
-                return display_name, str(best_dist)
+                return display_name, str(best_dist), is_mixed
             else:
-                return "No match found", str(best_dist)
+                return "No match found", str(best_dist), is_mixed
 
         except Exception as e:
-            return f"Error ({e})", "-"
+            return f"Error ({e})", "-", False
 
     def get_contig_stats(self, fasta_path):
         lengths = []
@@ -107,10 +122,9 @@ def get_contig_stats(self, fasta_path):
                 lengths.append(len(s))
                 ambiguous_count += sum(1 for b in s if b.upper() not in "ATCG")
 
-        if not lengths: return 0, 0, 0, 0, "no"
+        if not lengths: return 0, 0, 0, "no"
 
         lengths.sort()
-        longest = lengths[-1]
         total = sum(lengths)
         half = total / 2
         cum_sum = 0
@@ -122,4 +136,4 @@ def get_contig_stats(self, fasta_path):
                 break
 
         ambig_str = f"yes ({ambiguous_count})" if ambiguous_count > 0 else "no"
-        return len(lengths), n50, longest, total, ambig_str
+        return len(lengths), n50, total, ambig_str