def test_write_file_yaml(tmpdir):
"""Test write_file YAML file output."""
path = tmpdir.mkdir("sub").join("outfile.yaml")
pathname = abspath(path)
tofile.write_file(pathname, VALUE)
assert len(tmpdir.listdir()) == 1
assert path.read() == EXAMPLE_YAML
tmpdir.remove()
def test_write_file_json(tmpdir):
"""Test write_file JSON file output."""
path = tmpdir.mkdir("sub").join("outfile.json")
pathname = abspath(path)
tofile.write_file(pathname, VALUE)
assert len(tmpdir.listdir()) == 1
assert path.read() == EXAMPLE_JSON
tmpdir.remove()
def test_write_file_yaml_gz(tmpdir):
"""Test write_file gzipped YAML output."""
path = tmpdir.mkdir("sub").join("outfile.yaml.gz")
pathname = abspath(path)
tofile.write_file(pathname, VALUE)
assert len(tmpdir.listdir()) == 1
with open(pathname, "rb") as fh:
assert binascii.hexlify(fh.read(2)) == b"1f8b"
tmpdir.remove()
def test_write_file_plain(tmpdir):
"""Test write_file text file output."""
path = tmpdir.mkdir("sub").join("outfile.txt")
pathname = abspath(path)
example_string = "file content\n"
tofile.write_file(pathname, example_string)
assert len(tmpdir.listdir()) == 1
assert path.read() == example_string
tmpdir.remove()
def test_write_file_invalid_path():
"""Test write_file to bad path."""
example_string = "file content\n"
assert tofile.write_file("path/does/not/exist", example_string) is False
assert tofile.write_file("path/does/not/exist.gz", example_string) is False
def main():
"""Entry point."""
opts = docopt(__doc__)
accession = opts["<ACCESSION>"]
outdir = opts["--out"]
dbdir = opts["--db"]
buscodir = "%s/busco" % dbdir
uniprotdir = "%s/uniprot" % dbdir
ntdir = "%s/nt" % dbdir
taxdumpdir = "%s/taxdump" % dbdir
if opts["--db-suffix"]:
buscodir += "_%s" % opts["--db-suffix"]
ntdir += "_%s" % opts["--db-suffix"]
uniprotdir += "_%s" % opts["--db-suffix"]
taxdumpdir += "_%s" % opts["--db-suffix"]
if not outdir.endswith(accession):
outdir += "/%s" % accession
os.makedirs(outdir, exist_ok=True)
meta = parse_assembly_meta(accession)
assembly_url = fetch_assembly_url(accession, opts["--api-key"])
if assembly_url is None:
LOGGER.error("Unable to find assembly URL")
sys.exit(1)
assembly_file = "%s/assembly/%s.fasta.gz" % (outdir, accession)
meta["assembly"].update({"file": assembly_file, "url": assembly_url})
assembly_report = "%s/assembly/%s.report.txt" % (outdir, accession)
syn_filename = "%s/assembly/%s.synonyms.tsv" % (outdir, accession)
cat_filename = "%s/assembly/%s.categories.tsv" % (outdir, accession)
meta["fields"] = {
"synonyms": {
"file": syn_filename,
"prefix": "insdc"
},
"categories": {
"file": cat_filename
},
}
if opts["--download"]:
os.makedirs(buscodir, exist_ok=True)
os.makedirs("%s/assembly" % outdir, exist_ok=True)
fetch_assembly_fasta(assembly_url, assembly_file)
report_url = assembly_url.replace("_genomic.fna.gz",
"_assembly_report.txt")
fetch_assembly_report(report_url, assembly_report, cat_filename,
syn_filename)
taxon_meta = fetch_goat_data(meta["taxon"]["taxid"])
add_taxon_to_meta(meta, taxon_meta)
set_btk_version(meta)
busco_sets = find_busco_lineages(taxon_meta["lineage"])
if busco_sets:
meta["busco"].update({
"download_dir":
buscodir,
"lineages":
busco_sets,
"basal_lineages": [
"eukaryota_odb10",
"bacteria_odb10",
"archaea_odb10",
],
})
if opts["--download"]:
fetch_busco_lineages(busco_sets, buscodir)
read_accessions = []
if meta["assembly"]["biosample"]:
read_accessions = [meta["assembly"]["biosample"]]
if opts["--reads"]:
read_accessions += opts["--reads"]
sra = assembly_reads(read_accessions, int(opts["--read-runs"]),
opts["--platforms"])
if sra:
if opts["--coverage"]:
meta["reads"].update(
{"coverage": {
"max": int(opts["--coverage"])
}})
readdir = "%s/reads" % outdir
add_reads_to_meta(meta, sra, readdir)
if opts["--download"]:
os.makedirs(readdir, exist_ok=True)
for library in sra:
fetch_read_files(library)
meta["similarity"]["blastn"].update({"path": ntdir})
meta["similarity"]["diamond_blastx"].update({"path": uniprotdir})
meta["similarity"]["diamond_blastp"].update({"path": uniprotdir})
meta["settings"]["taxdump"] = taxdumpdir
tofile.write_file("%s/config.yaml" % outdir, meta)
def parse_assembly_report(filename, cat_filename, syn_filename):
"""Parse synonyms and assembly level into tsv files."""
synonyms = []
categories = []
cats = {
"identifier": {
"index": 4,
"list": []
},
"assembly_role": {
"index": 1,
"list": []
},
"assembly_level": {
"index": 3,
"list": []
},
"assembly_unit": {
"index": 7,
"list": []
},
}
names = {
"identifier": {
"index": 4,
"list": []
},
"name": {
"index": 0,
"list": []
},
"assigned_name": {
"index": 2,
"list": []
},
"refseq_accession": {
"index": 6,
"list": []
},
}
with tofile.open_file_handle(filename) as fh:
for line in fh:
if line.startswith("#"):
continue
row = line.rstrip().split("\t")
for group in (cats, names):
for obj in group.values():
value = row[obj["index"]]
obj["list"].append(value)
header = []
for key, obj in cats.items():
if len(set(obj["list"])) > 1:
header.append(key)
categories.append(header)
for idx, value in enumerate(cats[header[0]]["list"]):
row = [value]
for key in header[1:]:
row.append(cats[key]["list"][idx])
categories.append(row)
tofile.write_file(cat_filename, categories)
header = []
for key, obj in names.items():
if len(set(obj["list"])) > 1:
header.append(key)
synonyms.append(header)
for idx, value in enumerate(names[header[0]]["list"]):
row = [value]
for key in header[1:]:
row.append(names[key]["list"][idx])
synonyms.append(row)
tofile.write_file(syn_filename, synonyms)
"bacteria_odb10",
"archaea_odb10",
],
})
if opts["--download"]:
fetch_busco_lineages(busco_sets, buscodir)
read_accessions = []
if meta["assembly"]["biosample"]:
read_accessions = [meta["assembly"]["biosample"]]
if opts["--reads"]:
read_accessions += opts["--reads"]
sra = assembly_reads(read_accessions, int(opts["--read-runs"]),
opts["--platforms"])
if sra:
if opts["--coverage"]:
meta["reads"].update(
{"coverage": {
"max": int(opts["--coverage"])
}})
readdir = "%s/reads" % outdir
add_reads_to_meta(meta, sra, readdir)
if opts["--download"]:
os.makedirs(readdir, exist_ok=True)
for library in sra:
fetch_read_files(library)
meta["similarity"]["blastn"].update({"path": ntdir})
meta["similarity"]["diamond_blastx"].update({"path": uniprotdir})
meta["similarity"]["diamond_blastp"].update({"path": uniprotdir})
meta["settings"]["taxdump"] = taxdumpdir
tofile.write_file("%s/config.yaml" % outdir, meta)