Update fasta_generate_regions.py to work with Snakemake example

Use ceil() instead of round() to prevent round-off errors from affecting regions/numbering

examples/snakemake-freebayes-parallel.smk

@@ -1,7 +1,7 @@
 ## A simple example snakemake .smk file for parallelising freebayes
 ## Uses a fasta_generate_regions to split the genome into regions of equal size based on the .fai index
 ## As snakemake automatically moves each cpu core to the next genome chunk, this works out faster
-## than the freebayes-parallel wrapper and allows pooled sample calling. 
+## than the freebayes-parallel wrapper.
 ## This .smk file assumes we have a list of the bam files called bam.list
 ## This .smk file splits the genome by chromosome, which of course, is not necessary.
 ## One will want to edit the paths (for example, the path to bam files)
@@ -14,7 +14,7 @@ chroms = [1,2,3]
 nchunks = 9
 
 bamlist = "path/to/bam.list"
-chunks = [i for i in range(1,nchunks+1)]
+chunks = list(range(1,nchunks+1))
 
 rule GenomeIndex:
     input:

scripts/fasta_generate_regions.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
 import argparse
+from math import ceil
 
 
 def generate_regions(fasta_index_file, size, chunks=False, chromosomes=None, bed_files=None):
@@ -17,7 +18,7 @@ def generate_regions(fasta_index_file, size, chunks=False, chromosomes=None, bed
                 continue
             region_start = 0
             if chunks is True:
-                region_size = round(chrom_length / size)  # have to make sure this works
+                region_size = ceil(chrom_length / size)  # have to make sure this works
             else:
                 region_size = size
             while region_start < chrom_length:
@@ -27,7 +28,7 @@ def generate_regions(fasta_index_file, size, chunks=False, chromosomes=None, bed
                 start = str(region_start)
                 end = str(region_end)
                 if bed_files is not None:
-                    region = str(round(region_end / region_size))
+                    region = str(ceil(region_end / region_size))
                     file_path = f"{bed_files}.{chrom_name}.region.{region}.bed"
                     with open(file_path, "w") as f:
                         f.write("\t".join([chrom_name, start, end]))