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utils.py
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utils.py
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"""Define static variables and utilities functions used throughout CRISPRme.
"""
import sys
import os
CRISPRME_DIRS = [
"Genomes",
"Results",
"Dictionaries",
"VCFs",
"Annotations",
"PAMs",
"samplesIDs",
]
def check_directories(basedir: str) -> None:
"""The function checks the consistency of CRISPRme's directory tree.
If a directory is not found in the tree, it will be created.
...
Parameters
----------
basedir : str
Base directory
Returns
-------
None
"""
if not isinstance(basedir, str):
raise TypeError(f"Expected {str.__name__}, got {type(basedir).__name__}")
if not os.path.exists(basedir):
raise FileNotFoundError(f"Unable to locate {basedir}")
for d in CRISPRME_DIRS:
if not os.path.exists(os.path.join(basedir, d)):
os.makedirs(os.path.join(basedir, d))
def download_genome(chr: str, directory: str) -> None:
if not isinstance(chr, str):
raise TypeError(f"Expected {str.__name__}, got {type(chr).__name__}")
if not isinstance(directory, str):
raise TypeError(f"Expected {str.__name__}, got {type(directory).__name__}")
if chr == "all":
os.system(
"wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz -O hg38.chromFa.tar.gz"
)
os.system("mv hg38.chromFa.tar.gz Genomes/")
os.system("tar -xzf Genomes/hg38.chromFa.tar.gz")
os.system(f"mv Genomes/chroms mv Genomes/{directory}")
else:
os.system(
f"wget https://hgdownload2.soe.ucsc.edu/goldenPath/hg38/chromosomes/{chr}.fa.gz -O {chr}.fa.gz"
)
os.system(f"mv {chr}.fa.gz Genomes/")
os.system(f"gunzip Genomes/{chr}.fa.gz")
os.makedirs(f"Genomes/{directory}", exist_ok=True)
os.system(f"mv Genomes/{chr}.fa Genomes/{directory}/{chr}.fa")
def download_vcf(chr: str, origin: str) -> None:
if not isinstance(chr, str):
raise TypeError(f"Expected {str.__name__}, got {type(chr).__name__}")
if not isinstance(origin, str):
raise TypeError(f"Expected {str.__name__}, got {type(origin).__name__}")
if chr == "all" and origin == "1000G":
os.makedirs(f"VCFs/hg38_1000G", exist_ok=True)
for i in range(1, 23):
os.system(
f"wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz -O ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz"
)
os.system(
f"mv ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz VCFs/hg38_1000G/"
)
elif chr != "all" and origin == "1000G":
os.makedirs(f"VCFs/hg38_1000G", exist_ok=True)
os.system(
f"wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.{chr}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz -O ALL.{chr}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz"
)
os.system(
f"mv ALL.{chr}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz VCFs/hg38_1000G/"
)
elif chr == "all" and origin == "HGDP":
os.makedirs(f"VCFs/hg38_HGDP", exist_ok=True)
for i in range(1, 23):
os.system(
f"wget ftp://ngs.sanger.ac.uk:21/production/hgdp/hgdp_wgs.20190516/hgdp_wgs.20190516.full.chr{i}.vcf.gz -O hgdp_wgs.20190516.full.chr{i}.vcf.gz"
)
os.system(f"mv hgdp_wgs.20190516.full.chr{i}.vcf.gz VCFs/hg38_HGDP/")
elif chr != "all" and origin == "HGDP":
os.makedirs(f"VCFs/hg38_HGDP", exist_ok=True)
os.system(
f"wget ftp://ngs.sanger.ac.uk:21/production/hgdp/hgdp_wgs.20190516/hgdp_wgs.20190516.full.{chr}.vcf.gz -O hgdp_wgs.20190516.full.{chr}.vcf.gz"
)
os.system(f"mv hgdp_wgs.20190516.full.{chr}.vcf.gz VCFs/hg38_HGDP/")
def download_samplesID() -> None:
os.system(
"wget https://raw.githubusercontent.com/pinellolab/CRISPRme/test-function/download_data/hg38_1000G.samplesID.txt -O hg38_1000G.samplesID.txt"
)
os.system(
"wget https://raw.githubusercontent.com/pinellolab/CRISPRme/test-function/download_data/hg38_HGDP.samplesID.txt -O hg38_HGDP.samplesID.txt"
)
os.system(
"wget https://raw.githubusercontent.com/pinellolab/CRISPRme/test-function/download_data/hg38_gnomAD.samplesID.txt -O hg38_gnomAD.samplesID.txt"
)
os.system("mv hg38_1000G.samplesID.txt samplesIDs/")
os.system("mv hg38_HGDP.samplesID.txt samplesIDs/")
os.system("mv hg38_gnomAD.samplesID.txt samplesIDs/")
def download_annotation() -> None:
os.system(
"wget https://github.com/pinellolab/CRISPRme/raw/test-function/download_data/gencode.protein_coding.tar.gz -O gencode.protein_coding.tar.gz"
)
os.system("tar -xzf gencode.protein_coding.tar.gz")
os.system("rm gencode.protein_coding.tar.gz")
os.system("mv gencode.protein_coding.bed Annotations/")
os.system(
"wget https://github.com/pinellolab/CRISPRme/raw/test-function/download_data/encode+gencode.hg38.tar.gz -O encode+gencode.hg38.tar.gz"
)
os.system("tar -xzf encode+gencode.hg38.tar.gz")
os.system("rm encode+gencode.hg38.tar.gz")
os.system("mv encode+gencode.hg38.bed Annotations/")