def run(self) -> List[str]:
self.carried_output: List[str] = []
create_output_dir(self.context.output)
self.context.threads = str(self.context.threads)
self.context.percent = str(self.context.percent)
self.context.taxa = str(get_taxa_from_contigs(self.context.contigs))
self.context.taxon_group = "all"
self.output_dirs = {
"match_contigs": "uce-search-results",
"match_counts": "all-taxa.conf",
"incomplete_matrix": "all-taxa.incomplete",
"fasta": "all-taxa.fasta",
"exploded_fastas": "exploded-fastas",
"alignments": "alignments",
"alignments_clean": "alignments-clean",
"gblocks": "alignments-gblocks",
"min_taxa": "alignments-gblocks-clean-min-taxa",
"raxml": "alignments-raxml",
}
# Prefixing with context output
for k, v in self.output_dirs.items():
self.output_dirs[k] = f"{self.context.output}/{v}"
self.context.locus_db = self.output_dirs[
"match_contigs"] + "/probe.matches.sqlite"
self.context.taxon_list_config = f"{self.context.output}/taxon-list.conf"
taxon_list_config_dict = parse_taxon_list_config(
self.context.contigs, self.context.taxon_group)
dump_config_file(self.context.taxon_list_config,
taxon_list_config_dict)
self._match_contigs_to_probes()
self._get_match_counts()
self._get_fastas_from_match_counts()
self._explode_get_fastas_file()
self._secap_align()
if self.context.internal_trimming:
self._get_gblocks_trimmed_alignments_from_untrimmed()
self._remove_locus_name_from_nexus_lines()
self._get_only_loci_with_min_taxa()
self._nexus_files_to_raxml()
return self.carried_output
def run(self) -> List[str]:
delete_output_dir_if_exists(self.context.output)
# Create and save the configuration file
config = "illumiprocessor.conf"
csv = load_csv(self.context.csv_file)
config_dict = parse_illumiprocessor_config(
csv, double_index=not self.context.single_index)
dump_config_file(config, config_dict)
cmd = [
"--input",
self.context.raw_fastq,
"--output",
self.context.output,
"--cores",
str(self.context.threads),
"--config",
config,
"--log-path",
self.context.log_dir,
]
if self.context.min_len:
cmd.extend(["--min-len", str(self.context.min_len)])
if self.context.r1_pattern:
cmd.extend(["--r1-pattern", self.context.r1_pattern])
if self.context.r2_pattern:
cmd.extend(["--r2-pattern", self.context.r2_pattern])
if self.context.phred64:
cmd.extend(["--phred", "phred64"])
if self.context.single_end:
cmd.append("--se")
if self.context.no_merge:
cmd.append("--no-merge")
return self.adapters["illumiprocessor"](
cmd, capture_output=self.context.capture_output)
def run(self) -> List[str]:
delete_output_dir_if_exists(self.context.output)
# Create and save the configuration file
if not self.context.config:
self.context.config = "assembly.conf"
config_dict = parse_assembly_config(self.context.clean_fastq)
dump_config_file(self.context.config, config_dict)
cmd = [
"--output",
self.context.output,
"--cores",
str(self.context.threads),
"--config",
self.context.config,
"--log-path",
self.context.log_dir,
]
if self.context.assembler == "spades":
if self.context.no_clean:
cmd.append("--do-not-clean")
if self.context.kmer:
cmd.extend(["--kmer", str(self.context.kmer)])
elif self.context.assembler == "trinity":
if not self.context.no_clean:
cmd.append("--clean")
if self.context.kmer:
cmd.extend(["--min-kmer-coverage", str(self.context.kmer)])
if self.context.subfolder:
cmd.extend(["--subfolder", self.context.subfolder])
return self.adapters[self.context.assembler](
cmd, capture_output=self.context.capture_output)
def run(self) -> List[CommandResult]:
delete_output_dir_if_exists(self.context.output)
# Create and save the configuration file
if not self.context.config:
self.context.config = "assembly.conf"
config_dict = parse_assembly_config(self.context.clean_fastq)
dump_config_file(self.context.config, config_dict)
cmd = [
"--output",
self.context.output,
"--cores",
str(self.context.threads),
"--config",
self.context.config,
"--log-path",
self.context.log_dir,
]
if self.context.subfolder:
cmd.extend(["--subfolder", self.context.subfolder])
self._parse_command(cmd)
return [self.adapters[self.context.assembler](cmd)]
def test_config_file_is_created(context, config_example):
dump_config_file(context["output"] + "test.conf", config_example[0])
with open(context["output"] + "test.conf", "r") as fl:
assert fl.read() == config_example[1]
def test_config_file_is_created(context, config_example):
dump_config_file(context["output"] + "test.conf", config_example)
assert os.path.isfile(context["output"] + "test.conf")