rabbit fixes, better validation

Author: pdimens

harpy/_conda.py

@@ -34,7 +34,7 @@ def create_conda_recipes(outdir: str, envs: list=None) -> None:
         ],
         "demultiplex": [
             "bioconda::pheniqs",
-            "bioconda::pysam",
+            "bioconda::pysam=0.22",
             "conda-forge::python-levenshtein"
         ],
         "metassembly": [

harpy/_printing.py

@@ -101,7 +101,7 @@ def print_onerror(logfile):
     console.print(f"The workflow stopped because of an error. Full workflow log:\n[bold]{logfile}[/bold]")
     console.rule("[bold]Where Error Occurred", style = "red")
 
-def workflow_info(*arg):
+def workflow_info(*arg: tuple[str, str | int | float]) -> Table:
     """
     Accepts an unlimited number of length-2 lists or tuples and returns a rich.Table with the value of the first indices as the row names and the second indices as the values
     Use None instead of a list to ignore that entry (useful for conditionals). The second value will always be converted to a string.

harpy/_validations.py

@@ -257,17 +257,32 @@ def validate_popsamples(infiles, popfile, quiet):
 
 def validate_demuxschema(infile):
     """Validate the file format of the demultiplex schema"""
-    with open(infile, "r", encoding="utf-8") as f:
-        rows = [i for i in f.readlines() if i != "\n" and not i.lstrip().startswith("#")]
-        invalids = [(i,j) for i,j in enumerate(rows) if len(j.split()) < 2]
-        if invalids:
-            print_error(f"invalid format", "There are [bold]{len(invalids)}[/bold] rows in [blue]{infile}[/blue] without a space/tab delimiter or don't have two entries for sample[dim]<tab>[/dim]barcode. Terminating Harpy to avoid downstream errors.")
-            print_solution_with_culprits(
-                f"Make sure every entry in [blue]{infile}[/blue] uses space or tab delimeters and has both a sample name and barcode designation. You may comment out rows with a [green]#[/green] to have Harpy ignore them.",
-                "The rows and values causing this error are:"
-                )
-            _ = [click.echo(f"{i[0]+1}\t{i[1]}", file = sys.stderr) for i in invalids]
-            sys.exit(1)
+    code_letters = set() #codes can be Axx, Bxx, Cxx, Dxx
+    segment_ids = set()
+    with open(infile, 'r') as file:
+        for line in file:
+            try:
+                sample, segment_id = line.rstrip().split()
+                code_letters.add(segment_id[0])
+                if segment_id in segment_ids:
+                    print_error("An ID segment must only be associated with a single sample.")
+                    print_solution_with_culprits(
+                        "A barcode segment can only be associated with a single sample. For example, [green]C05[/green] cannot not be the segment that identifies both [blue]sample_01[/blue] and [blue]sample_2[/blue].",
+                        "The segment triggering this error is:"
+                        )
+                    click.echo(segment_id)
+                    sys.exit(1)
+                else:
+                    segment_id.add(seg_id)
+            except ValueError:
+                # skip rows without two columns
+                continue
+    if not code_letters:
+        print_error("incorrect schema format", f"Schema file {os.path.basename(infile)} has no valid rows. Rows should be sample<tab>segment, e.g. sample_01<tab>C75")
+        sys.exit(1)
+    if len(code_letters) > 1:
+        print("invalid schema", f"Schema file {os.path.basename(file_path)} has sample IDs expected to be indentified across multiple barcode segments. All sample IDs for this technology should be in a single segment, such as [bold green]C[/bold green] or [bold green]D[/bold green].")
+        sys.exit(1)
 
 def validate_regions(regioninput, genome):
     """validates the --regions input of harpy snp to infer whether it's an integer, region, or file"""

harpy/align.py

@@ -139,7 +139,7 @@ def bwa(inputs, output_dir, genome, depth_window, threads, keep_unmapped, extra_
     if setup_only:
         sys.exit(0)
 
-    start_text = (
+    start_text = workflow_info(
         ("Samples:",sample_count),
         ("Genome:", genome),
         ("Output Folder:", output_dir + "/"),

harpy/scripts/demultiplex_gen1.py

@@ -14,7 +14,8 @@ def read_barcodes(file_path, segment):
             try:
                 code, seq = line.rstrip().split()
                 if code[0].upper() != segment:
-                    parser.error(f"Segments in {file_path} are expected to begin with {segment}, but begin with {code[0].upper()}")
+                    sys.stderr.write(f"Segments in {file_path} are expected to begin with {segment}, but begin with {code[0].upper()}\n")
+                    sys.exit(1)
                 data_dict[seq] = code
             except ValueError:
                 # skip rows without two columns