fixed order of columns in splitvariants.py

src/sv-pipeline/04_variant_resolution/scripts/split_variants.py

@@ -28,12 +28,13 @@ def process_bed_file(input_bed, n_per_split, bca=True):
     with open(input_bed, 'r') as infile:
         for line in infile:
             # process bed file line by line
-            line = line.strip().split('\t')
+            line = line.strip('\n').split('\t')
 
             # Checks which condition and prefix the current line matches and appends it to the corresponding
             # array and increments the counter for that array
             for prefix, conditions in condition_prefixes.items():
                 if conditions['condition'](line):
+                    line[4],line[5]=line[5],line[4]
                     current_lines[prefix].append('\t'.join(line))
                     current_counts[prefix] += 1
 
@@ -61,19 +62,6 @@ def process_bed_file(input_bed, n_per_split, bca=True):
             logging.info(f"File '{output_file}' written.")
 
 
-# Function to generate the pattern for suffixes
-def increment_suffix(suffix):
-    # define the alphabet and ending
-    alphabet = 'abcdefghijklmnopqrstuvwxyz'
-    if suffix == 'z' * 6:
-        raise ValueError('All possible files generated.')
-    else:
-        # if there are available suffixes increment to next available suffix
-        index = alphabet.index(suffix[0])
-        next_char = alphabet[(index + 1) % 26]
-        return next_char + suffix[1:]
-
-
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument("--bed", help="Path to input bed file", required=True)