Release/v0.2.0

.gitignore

@@ -172,3 +172,6 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+
+*.DS_Store
+src/.DS_Store

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "HammingdistanceCalculator"
-version = "0.1.0"
+version = "0.2.0"
 description = "Script that calculates the hamming distance between a list of barcodes."
 readme = "README.md"
 authors = [
@@ -31,3 +31,7 @@ dev = [
 
 [tool.ruff]
 line-length = 127
+
+[tool.ruff.lint]
+select = ["E", "F", "W"]
+extend-select = ["W292"]

src/hammingdistancecalculator/hamming_distance.py

@@ -1,4 +1,3 @@
-import pathlib
 import re
 import typer
 import csv
@@ -35,11 +34,16 @@ def hamming_distance(seq1: str, seq2: str) -> int:
     check_1 = is_valid_dna(seq1)
     check_2 = is_valid_dna(seq2)
     if not check_1 and not check_2:
-        raise ValueError(f'Provided sequences are invalid, only A, C, T, and G nucleotides are allowed. Invalid sequences: {seq1}, {seq2}')
+        raise ValueError(
+            f'Provided sequences are invalid, only A, C, T, and G nucleotides are allowed. Invalid sequences: {seq1}, {seq2}')
     elif not check_1 and check_2:
-        raise ValueError(f'Provided sequence for sequence 1 is invalid, only A, C, T, and G nucleotides are allowed. Invalid sequence: {seq1}')
+        raise ValueError(
+            f'Provided sequence for sequence 1 is invalid, only A, C, T, and G nucleotides are allowed. '
+            f'Invalid sequence: {seq1}')
     elif check_1 and not check_2:
-        raise ValueError(f'Provided sequence for sequence 2 is invalid, only A, C, T, and G nucleotides are allowed. Invalid sequence: {seq2}')
+        raise ValueError(
+            f'Provided sequence for sequence 2 is invalid, only A, C, T, and G nucleotides are allowed. '
+            f'Invalid sequence: {seq2}')
 
     # break if index have unequal length
     if len(seq1) != len(seq2):
@@ -57,7 +61,6 @@ def hamming_distance(seq1: str, seq2: str) -> int:
 
 def is_valid_dna(seq: str) -> bool:
     """Check if provided dna string contains valid characters
-
     Currently only 'A', 'C', 'T' and 'G' are checked for.
 
     Args:
@@ -72,7 +75,6 @@ def is_valid_dna(seq: str) -> bool:
 
 def rev_comp(dna: str) -> str:
     """Function which returns the reverse complement of a DNA string
-
     Args:
         dna: The input DNA string we want to convert
 
@@ -89,7 +91,6 @@ def rev_comp(dna: str) -> str:
 
 def is_valid_input_csv(csv_file: Path) -> bool:
     """Function that tests input csv file given to be in the expected format.
-
     We expect the file to have a header with labels 'label', 'barcode'.
     We expect no empty labels
     We expect no empty barcodes
@@ -215,8 +216,13 @@ def main(input_csv: Path = typer.Argument(help="Pad naar input CSV met kolommen:
              "--max-distance",
              "-d",
              help="Maximale hamming distance waarvoor output wordt geschreven (default op 1, wat 0 & 1 schrijft)."
+         ),
+         outpath: Path = typer.Option(
+             ".",
+             "--outpath",
+             "-o",
+             help="Directory waar output files worden geschreven (default huidige directory)."
          )):
-
     # read input
     sample_barcode_list = load_barcodes(input_csv)
 
@@ -233,17 +239,25 @@ def main(input_csv: Path = typer.Argument(help="Pad naar input CSV met kolommen:
     for key, value in compare_dict.items():
         hamming_distance_dict[value].append(key)
 
-    # write output files for all distances of 0 to max_distance (2 by default)
-    for counter in range(max_distance):
-        output_path = pathlib.Path(f"hamming_distance_{counter}.txt")
+    # verify output path exists to write to
+    outpath.mkdir(parents=True, exist_ok=True)
+
+    # add 1 to the max distance because when you want a range of 1, you want to loop 'including' 1, not 'until' 1
+    effective_max_distance = max_distance + 1
+
+    # write output files for all distances of 0 to effective_max_distance (2 by default)
+    for counter in range(effective_max_distance):
+        output_path = outpath / f"hamming_distance_{counter}.txt"
 
         # write each file
         with output_path.open('w', newline='') as file_handle:
             writer = csv.writer(file_handle)
-            writer.writerow([f"Number of comparisons found with hamming distance {counter}: {len(hamming_distance_dict[counter])}"])
+            writer.writerow(
+                [f"Number of comparisons found with hamming distance {counter}: {len(hamming_distance_dict[counter])}"])
 
             for item in hamming_distance_dict[counter]:
-                writer.writerow([f"Barcode {item.split('_vs_')[0]} vs barcode {item.split('_vs_')[1]} has hamming distance {counter}"])
+                writer.writerow(
+                    [f"Barcode {item.split('_vs_')[0]} vs barcode {item.split('_vs_')[1]} has hamming distance {counter}"])
 
 
 if __name__ == "__main__":