after black linting

Author: erinyoung

src/minkemap/__init__.py

@@ -1,2 +1 @@
-
-__version__ = "0.1.0"
+__version__ = "0.1.0"

src/minkemap/cli.py

@@ -12,67 +12,119 @@
     level=logging.INFO,
     format="%(asctime)s - %(levelname)s - %(message)s",
     datefmt="%H:%M:%S",
-    handlers=[logging.StreamHandler(sys.stderr)]
+    handlers=[logging.StreamHandler(sys.stderr)],
 )
 logger = logging.getLogger("MinkeMap")
 
+
 def main():
-    parser = argparse.ArgumentParser(description="MinkeMap: Circular Genome Visualization Tool")
-    
+    parser = argparse.ArgumentParser(
+        description="MinkeMap: Circular Genome Visualization Tool"
+    )
+
     # Meta
-    parser.add_argument("-v", "--version", action="version", version=f"MinkeMap v{__version__}")
-    
+    parser.add_argument(
+        "-v", "--version", action="version", version=f"MinkeMap v{__version__}"
+    )
+
     # Input / Output
-    parser.add_argument("-r", "--reference", required=True, help="Reference genome (FASTA or GenBank)")
-    parser.add_argument("-i", "--input", nargs="+", help="Input sequencing files (FASTQ/FASTA)")
-    parser.add_argument("-f", "--input-file", help="Manifest CSV file (cols: sample,read1,read2,type)")
-    parser.add_argument("-o", "--output", default="minkemap_plot.png", help="Output filename")
-    parser.add_argument("--outdir", default="minkemap_results", help="Directory to save all output files")
-    
+    parser.add_argument(
+        "-r", "--reference", required=True, help="Reference genome (FASTA or GenBank)"
+    )
+    parser.add_argument(
+        "-i", "--input", nargs="+", help="Input sequencing files (FASTQ/FASTA)"
+    )
+    parser.add_argument(
+        "-f", "--input-file", help="Manifest CSV file (cols: sample,read1,read2,type)"
+    )
+    parser.add_argument(
+        "-o", "--output", default="minkemap_plot.png", help="Output filename"
+    )
+    parser.add_argument(
+        "--outdir",
+        default="minkemap_results",
+        help="Directory to save all output files",
+    )
+
     # Aesthetics
-    parser.add_argument("--track-width", type=float, default=6, help="Width of each track ring (default: 6)")
-    parser.add_argument("--track-gap", type=float, default=4, help="Gap between tracks (default: 4)")
+    parser.add_argument(
+        "--track-width",
+        type=float,
+        default=6,
+        help="Width of each track ring (default: 6)",
+    )
+    parser.add_argument(
+        "--track-gap", type=float, default=4, help="Gap between tracks (default: 4)"
+    )
     parser.add_argument("--palette", default="whale", help="Color palette")
     parser.add_argument("--dpi", type=int, default=300, help="Image resolution")
     parser.add_argument("--title", help="Plot title")
-    parser.add_argument("--no-legend", action="store_true", help="Hide the sample legend")
-    parser.add_argument("--no-backbone", action="store_true", help="Hide the black reference backbone")
-    parser.add_argument("--label-size", type=int, default=6, help="Font size for gene/annotation labels")
-    
+    parser.add_argument(
+        "--no-legend", action="store_true", help="Hide the sample legend"
+    )
+    parser.add_argument(
+        "--no-backbone", action="store_true", help="Hide the black reference backbone"
+    )
+    parser.add_argument(
+        "--label-size", type=int, default=6, help="Font size for gene/annotation labels"
+    )
+
     # Features
-    parser.add_argument("--annotations", help="CSV file for custom regions (cols: reference,start,stop,label,color)")
-    parser.add_argument("--highlights", help="CSV file for background wedges (cols: start,end,color,label)")
-    parser.add_argument("--gc-skew", action="store_true", help="Add a GC Skew track to the center")
-    parser.add_argument("--no-save-data", action="store_true", help="Do not generate BED/CSV data files")
-    
+    parser.add_argument(
+        "--annotations",
+        help="CSV file for custom regions (cols: reference,start,stop,label,color)",
+    )
+    parser.add_argument(
+        "--highlights",
+        help="CSV file for background wedges (cols: start,end,color,label)",
+    )
+    parser.add_argument(
+        "--gc-skew", action="store_true", help="Add a GC Skew track to the center"
+    )
+    parser.add_argument(
+        "--no-save-data", action="store_true", help="Do not generate BED/CSV data files"
+    )
+
     # Filters
-    parser.add_argument("--min-identity", type=float, default=0, help="Minimum identity %% (0-100)")
-    parser.add_argument("--min-coverage", type=float, default=0, help="Minimum query coverage %% (0-100)")
-    parser.add_argument("--exclude-genes", help="Comma-separated list of terms to exclude from gene track (e.g. 'hypothetical,putative')")
+    parser.add_argument(
+        "--min-identity", type=float, default=0, help="Minimum identity %% (0-100)"
+    )
+    parser.add_argument(
+        "--min-coverage",
+        type=float,
+        default=0,
+        help="Minimum query coverage %% (0-100)",
+    )
+    parser.add_argument(
+        "--exclude-genes",
+        help="Comma-separated list of terms to exclude from gene track (e.g. 'hypothetical,putative')",
+    )
     parser.add_argument("--verbose", action="store_true", help="Enable debug logging")
 
     args = parser.parse_args()
-    
+
     if args.verbose:
         logger.setLevel(logging.DEBUG)
 
     min_id_decimal = args.min_identity / 100.0
     min_cov_decimal = args.min_coverage / 100.0
     should_save = not args.no_save_data
-    
+
     # 1. Create Output Directory & Log File
     try:
         os.makedirs(args.outdir, exist_ok=True)
         # Add File Handler to log to disk
         log_path = os.path.join(args.outdir, "minkemap.log")
-        file_handler = logging.FileHandler(log_path, mode='w')
-        file_handler.setFormatter(logging.Formatter("%(asctime)s - %(levelname)s - %(message)s"))
+        file_handler = logging.FileHandler(log_path, mode="w")
+        file_handler.setFormatter(
+            logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
+        )
         logger.addHandler(file_handler)
-        
+
         if args.outdir != ".":
             logger.info(f"Output directory: {args.outdir}/")
             logger.info(f"Log file: {log_path}")
-            
+
     except OSError as e:
         logger.error(f"Error creating directory {args.outdir}: {e}")
         sys.exit(1)
@@ -84,26 +136,30 @@ def main():
         sys.exit(1)
 
     total_tracks = len(samples)
-    if args.gc_skew: total_tracks += 1
-    total_tracks += 1 # Genes
-    if args.annotations: total_tracks += 1
-    
+    if args.gc_skew:
+        total_tracks += 1
+    total_tracks += 1  # Genes
+    if args.annotations:
+        total_tracks += 1
+
     # 3. Init Ring
     ring = GenomeRing(
-        args.reference, 
+        args.reference,
         outdir=args.outdir,
         track_width=args.track_width,
         track_gap=args.track_gap,
         palette=args.palette,
         total_tracks=total_tracks,
         no_backbone=args.no_backbone,  # <--- New Arg
-        label_size=args.label_size     # <--- New Arg
+        label_size=args.label_size,  # <--- New Arg
     )
-    
+
     logger.info(f"Reference loaded. Mapping {len(samples)} samples...")
     if args.min_identity > 0 or args.min_coverage > 0:
-        logger.info(f"   (Filters: Identity >= {args.min_identity}%, Coverage >= {args.min_coverage}%)")
-    
+        logger.info(
+            f"   (Filters: Identity >= {args.min_identity}%, Coverage >= {args.min_coverage}%)"
+        )
+
     # 4. Features
     if args.highlights:
         ring.add_highlights(args.highlights)
@@ -114,36 +170,45 @@ def main():
     # 5. Map & Draw
     for sample in samples:
         hits = map_sample(
-            ring.ref_path, 
-            sample, 
-            min_identity=min_id_decimal, 
-            min_coverage=min_cov_decimal
+            ring.ref_path,
+            sample,
+            min_identity=min_id_decimal,
+            min_coverage=min_cov_decimal,
         )
-        
-        is_reads = sample.seq_type.lower() in ["nanopore", "illumina", "illumina_paired_end", "pacbio", "hifi"]
+
+        is_reads = sample.seq_type.lower() in [
+            "nanopore",
+            "illumina",
+            "illumina_paired_end",
+            "pacbio",
+            "hifi",
+        ]
         plot_mode = "coverage" if is_reads else "rect"
-        
+
         ring.add_track(
-            sample.name, 
-            hits, 
-            plot_type=plot_mode, 
+            sample.name,
+            hits,
+            plot_type=plot_mode,
             min_identity=min_id_decimal,
             min_coverage=min_cov_decimal,
-            save_data=should_save
+            save_data=should_save,
         )
 
     # 6. Genes (with filtering)
-    exclude_list = [x.strip() for x in args.exclude_genes.split(',')] if args.exclude_genes else []
+    exclude_list = (
+        [x.strip() for x in args.exclude_genes.split(",")] if args.exclude_genes else []
+    )
     ring.add_genes_track(exclude_list=exclude_list)
-    
+
     if args.annotations:
         ring.add_custom_track(args.annotations)
 
     # 7. Save
     ring.save(args.output, dpi=args.dpi, title=args.title, no_legend=args.no_legend)
-    
+
     full_output_path = os.path.join(args.outdir, args.output)
     logger.info(f"Done! Saved to {full_output_path}")
 
+
 if __name__ == "__main__":
-    main()
+    main()