def split_vcf(in_file, config, out_dir=None):
"""
split a VCF file into separate files by chromosome
requires tabix to be installed
"""
if out_dir is None:
out_dir = os.path.join(os.path.dirname(in_file), "split")
fasta_file = config["ref"]["fasta"]
fasta_index = fasta_file + ".fai"
samtools_path = config["program"].get("samtools", "samtools")
tabix_path = config["program"].get("tabix", "tabix")
if not file_exists(fasta_index):
samtools = sh.Command(samtools_path)
samtools.faidx(fasta_file)
# if in_file is not compressed, compress it
(_, ext) = os.path.splitext(in_file)
if ext is not ".gz":
gzip_file = in_file + ".gz"
if not file_exists(gzip_file):
sh.bgzip("-c", in_file, _out=gzip_file)
in_file = gzip_file
# create tabix index
tabix_index(in_file)
# find the chromosome names from the fasta index file
chroms = str(sh.cut("-f1", fasta_index)).split()
# make outfile from chromosome name
def chr_out(chrom):
out_file = replace_suffix(append_stem(in_file, chrom), ".vcf")
return os.path.join(out_dir, os.path.basename(out_file))
# run tabix to break up the vcf file
def run_tabix(chrom):
tabix = sh.Command(tabix_path)
out_file = chr_out(chrom)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tmp_out_file:
tabix("-h", in_file, chrom, _out=tmp_out_file)
return out_file
out_files = map(run_tabix, chroms)
return out_files
def index_gff(gff, compress):
"""Index and optionally compress a GFF file.
\b
Examples:
bionorm index_gff Medicago_truncatula/jemalong_A17.gnm5.ann1.FAKE/medtr.jemalong_A17.gnm5.ann1.FAKE.gene_models_main.gff3
"""
from sh import bgzip # isort:skip
from sh import tabix # isort:skip
target = Path(gff)
if len(target.suffixes) < 1:
error_message = f"Target {target} does not have a file extension."
logger.error(error_message)
sys.exit(1)
if target.suffix.lstrip(".") in COMPRESSED_TYPES:
logger.error(f"Uncompress {target} befor indexing.")
sys.exit(1)
if target.suffix.lstrip(".") not in GFF_TYPES:
logger.error(
f"File {target} does not have a recognized GFF extension.")
sys.exit(1)
if compress:
output = bgzip(["-f", str(target)])
target = Path(target.parent) / f"{target.name}.gz"
output = tabix(["-p", "gff", str(target)])
output = tabix(["--csi", "-p", "gff", str(target)])
return target
def index_fasta(fasta, compress):
"""Index and optionally compress a fasta file.
\b
Examples:
bionorm index_fasta Medicago_truncatula/jemalong_A17.gnm5.ann1.FAKE/medtr.jemalong_A17.gnm5.FAKE.genome_main.fna
"""
from sh import bgzip # isort:skip
from sh import samtools # isort:skip
target = Path(fasta)
if len(target.suffixes) < 1:
error_message = f"Target {target} does not have a file extension."
logger.error(error_message)
sys.exit(1)
if target.suffix.lstrip(".") in COMPRESSED_TYPES:
logger.error(f"Uncompress {target} befor indexing.")
sys.exit(1)
if target.suffix.lstrip(".") not in FASTA_TYPES:
logger.error(
f"File {target} does not have a recognized FASTA extension.")
sys.exit(1)
if compress:
output = bgzip(["-f", "--index", str(target)])
target = Path(target.parent) / f"{target.name}.gz"
output = samtools(["faidx", str(target)])
return target
def _break_vcf(self, in_file):
if not file_exists(self.fasta_index):
sh.samtools.faidx(self.fasta_file)
# if file is not compressed, compress it
(_, ext) = os.path.splitext(in_file)
if ext is not ".gz":
gzip_file = in_file + ".gz"
sh.bgzip("-c", in_file, _out=gzip_file)
in_file = gzip_file
# create tabix index if it does not exist already
if not file_exists(in_file + ".tbi"):
sh.tabix("-p", "vcf", in_file)
# find the chromosome names from the fasta index file
chroms = str(sh.cut("-f1", self.fasta_index)).split()
break_dir = os.path.join(os.path.dirname(in_file), "break")
safe_makedir(break_dir)
def chr_out(chrom):
out_file = os.path.join(break_dir, append_stem(in_file, chrom))
out_file = replace_suffix(out_file, "vcf")
return out_file
def tabix(chrom):
out_file = chr_out(chrom)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tmp_out_file:
sh.tabix("-h", in_file, chrom, _out=tmp_out_file)
return out_file
# use tabix to separate out the variants based on chromosome
out_files = map(tabix, chroms)
return out_files
def _break_vcf(self, in_file):
if not file_exists(self.fasta_index):
sh.samtools.faidx(self.fasta_file)
# if file is not compressed, compress it
(_, ext) = os.path.splitext(in_file)
if ext is not ".gz":
gzip_file = in_file + ".gz"
sh.bgzip("-c", in_file, _out=gzip_file)
in_file = gzip_file
# create tabix index if it does not exist already
if not file_exists(in_file + ".tbi"):
sh.tabix("-p", "vcf", in_file)
# find the chromosome names from the fasta index file
chroms = str(sh.cut("-f1", self.fasta_index)).split()
break_dir = os.path.join(os.path.dirname(in_file), "break")
safe_makedir(break_dir)
def chr_out(chrom):
out_file = os.path.join(break_dir, append_stem(in_file, chrom))
out_file = replace_suffix(out_file, "vcf")
return out_file
def tabix(chrom):
out_file = chr_out(chrom)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tmp_out_file:
sh.tabix("-h", in_file, chrom, _out=tmp_out_file)
return out_file
# use tabix to separate out the variants based on chromosome
out_files = map(tabix, chroms)
return out_files
