def _validate_reads(self):
c = 0
for read_file in self.reads:
if not Utilities.is_file_valid(read_file, False):
print("Not found the raw read file: '{}'".format(read_file))
c += 1
self.is_valid = c == 0
def dump_index_guide(input_nucleotide_fasta: str, output_dir: str):
if not Utilities.is_file_valid(input_nucleotide_fasta):
raise ValueError(f"Invalid file: '{input_nucleotide_fasta}'")
cmd_0 = f"""
export IMG=ivasilyev/bwt_filtering_pipeline_worker:latest && \
docker pull "$IMG" && \
docker run --rm -v /data:/data -v /data1:/data1 -v /data2:/data2 -it "$IMG" \
bash -c '
cd "{output_dir}";
python3 "$HOME/scripts/cook_the_reference.py" \
--input "{input_nucleotide_fasta}" \
--output "{output_dir}";
'
"""
cmd = Utilities.join_lines(cmd_0)
out_file = os.path.join(output_dir, "index.sh")
Utilities.dump_string(cmd, out_file)
print(f"For indexing, run outside of Docker: 'bash \"{out_file}\"'")
