def install_annotation_files(anno_root_dir, dl_files=False, extra=None):
"""Download required annotation files.
"""
# create the full gemini data path based on
# the root dir the user provided
if anno_root_dir.endswith(("gemini/data", "gemini/data/", "gemini_data")):
anno_dir = anno_root_dir
elif anno_root_dir.endswith(("gemini", "gemini/")):
anno_dir = os.path.join(anno_root_dir, "data")
else:
anno_dir = os.path.join(anno_root_dir, "gemini", "data")
cur_config = read_gemini_config(allow_missing=True)
cur_config["annotation_dir"] = os.path.abspath(anno_dir)
cur_config["versions"] = anno_versions
write_gemini_config(cur_config)
if dl_files:
if not os.path.exists(anno_dir):
os.makedirs(anno_dir)
if not os.path.isdir(anno_dir):
sys.exit(anno_dir + " is not a valid directory.")
_check_dependencies()
to_dl = anno_files[:]
if extra:
to_dl += [extra_anno_files[x] for x in extra]
_download_anno_files("https://s3.amazonaws.com/gemini-annotations",
to_dl, anno_dir, cur_config)
def update_cosmic_census_genes(session, args):
"""
Update the gene summary table with
whether or not a given gene is in the
COSMIC cancer gene census
"""
config = read_gemini_config(args=args)
path_dirname = config["annotation_dir"]
file = os.path.join(path_dirname, "cancer_gene_census.20140120.tsv")
cosmic_census_genes = []
for line in open(file, "r"):
fields = line.strip().split("\t")
gene = fields[0]
chrom = "chr" + fields[3]
cosmic_census_genes.append((1, gene, chrom))
database_cassandra.update_gene_summary_w_cancer_census(session, cosmic_census_genes)
def update_cosmic_census_genes(session, args):
"""
Update the gene summary table with
whether or not a given gene is in the
COSMIC cancer gene census
"""
config = read_gemini_config(args=args)
path_dirname = config["annotation_dir"]
file = os.path.join(path_dirname, 'cancer_gene_census.20140120.tsv')
cosmic_census_genes = []
for line in open(file, 'r'):
fields = line.strip().split("\t")
gene = fields[0]
chrom = "chr" + fields[3]
cosmic_census_genes.append((1, gene, chrom))
database_cassandra.update_gene_summary_w_cancer_census(
session, cosmic_census_genes)
def get_anno_files( args ):
config = read_gemini_config( args = args )
anno_dirname = config["annotation_dir"]
# Default annotations -- always found
annos = {
'pfam_domain': os.path.join(anno_dirname, 'hg19.pfam.ucscgenes.bed.gz'),
'cytoband': os.path.join(anno_dirname, 'hg19.cytoband.bed.gz'),
'dbsnp': os.path.join(anno_dirname, 'dbsnp.b141.20140813.hg19.vcf.gz'),
'clinvar': os.path.join(anno_dirname, 'clinvar_20140807.vcf.gz'),
'gwas': os.path.join(anno_dirname, 'hg19.gwas.bed.gz'),
'rmsk': os.path.join(anno_dirname, 'hg19.rmsk.bed.gz'),
'segdup': os.path.join(anno_dirname, 'hg19.segdup.bed.gz'),
'conserved': os.path.join(anno_dirname, '29way_pi_lods_elements_12mers.chr_specific.fdr_0.1_with_scores.txt.hg19.merged.bed.gz'),
'cpg_island': os.path.join(anno_dirname, 'hg19.CpG.bed.gz'),
'dgv': os.path.join(anno_dirname, 'hg19.dgv.bed.gz'),
'esp': os.path.join(anno_dirname,
'ESP6500SI.all.snps_indels.vcf.gz'),
'1000g': os.path.join(anno_dirname,
'ALL.autosomes.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz'),
'recomb': os.path.join(anno_dirname,
'genetic_map_HapMapII_GRCh37.gz'),
'gms': os.path.join(anno_dirname,
'GRCh37-gms-mappability.vcf.gz'),
'grc': os.path.join(anno_dirname, 'GRC_patch_regions.bed.gz'),
'cse': os.path.join(anno_dirname, "cse-hiseq-8_4-2013-02-20.bed.gz"),
'encode_tfbs': os.path.join(anno_dirname,
'wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz'),
'encode_dnase1': os.path.join(anno_dirname,
'stam.125cells.dnaseI.hg19.bed.gz'),
'encode_consensus_segs': os.path.join(anno_dirname,
'encode.6celltypes.consensus.bedg.gz'),
'gerp_elements': os.path.join(anno_dirname, 'hg19.gerp.elements.bed.gz'),
'vista_enhancers': os.path.join(anno_dirname, 'hg19.vista.enhancers.20131108.bed.gz'),
'fitcons': os.path.join(anno_dirname, "hg19_fitcons_fc-i6-0_V1-01.bw"),
'cosmic': os.path.join(anno_dirname, 'cosmic-v68-GRCh37.vcf.gz'),
'exac': os.path.join(anno_dirname, 'ExAC.r0.2.sites.vep.vcf.gz')
}
# optional annotations
if os.path.exists(os.path.join(anno_dirname, 'hg19.gerp.bw')):
annos['gerp_bp'] = os.path.join(anno_dirname, 'hg19.gerp.bw')
if os.path.exists(os.path.join(anno_dirname, 'whole_genome_SNVs.tsv.compressed.gz')):
annos['cadd_score'] = os.path.join(anno_dirname, 'whole_genome_SNVs.tsv.compressed.gz')
return annos
#!/usr/bin/env python """ Store the path for GEMINI data-dir """ from geminicassandra.config import read_gemini_config config = read_gemini_config() anno_dirname = config["annotation_dir"] print anno_dirname
def get_anno_files(args):
config = read_gemini_config(args=args)
anno_dirname = config["annotation_dir"]
# Default annotations -- always found
annos = {
'pfam_domain':
os.path.join(anno_dirname, 'hg19.pfam.ucscgenes.bed.gz'),
'cytoband':
os.path.join(anno_dirname, 'hg19.cytoband.bed.gz'),
'dbsnp':
os.path.join(anno_dirname, 'dbsnp.b141.20140813.hg19.vcf.gz'),
'clinvar':
os.path.join(anno_dirname, 'clinvar_20140807.vcf.gz'),
'gwas':
os.path.join(anno_dirname, 'hg19.gwas.bed.gz'),
'rmsk':
os.path.join(anno_dirname, 'hg19.rmsk.bed.gz'),
'segdup':
os.path.join(anno_dirname, 'hg19.segdup.bed.gz'),
'conserved':
os.path.join(
anno_dirname,
'29way_pi_lods_elements_12mers.chr_specific.fdr_0.1_with_scores.txt.hg19.merged.bed.gz'
),
'cpg_island':
os.path.join(anno_dirname, 'hg19.CpG.bed.gz'),
'dgv':
os.path.join(anno_dirname, 'hg19.dgv.bed.gz'),
'esp':
os.path.join(anno_dirname, 'ESP6500SI.all.snps_indels.vcf.gz'),
'1000g':
os.path.join(
anno_dirname,
'ALL.autosomes.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz'
),
'recomb':
os.path.join(anno_dirname, 'genetic_map_HapMapII_GRCh37.gz'),
'gms':
os.path.join(anno_dirname, 'GRCh37-gms-mappability.vcf.gz'),
'grc':
os.path.join(anno_dirname, 'GRC_patch_regions.bed.gz'),
'cse':
os.path.join(anno_dirname, "cse-hiseq-8_4-2013-02-20.bed.gz"),
'encode_tfbs':
os.path.join(anno_dirname,
'wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz'),
'encode_dnase1':
os.path.join(anno_dirname, 'stam.125cells.dnaseI.hg19.bed.gz'),
'encode_consensus_segs':
os.path.join(anno_dirname, 'encode.6celltypes.consensus.bedg.gz'),
'gerp_elements':
os.path.join(anno_dirname, 'hg19.gerp.elements.bed.gz'),
'vista_enhancers':
os.path.join(anno_dirname, 'hg19.vista.enhancers.20131108.bed.gz'),
'fitcons':
os.path.join(anno_dirname, "hg19_fitcons_fc-i6-0_V1-01.bw"),
'cosmic':
os.path.join(anno_dirname, 'cosmic-v68-GRCh37.vcf.gz'),
'exac':
os.path.join(anno_dirname, 'ExAC.r0.2.sites.vep.vcf.gz')
}
# optional annotations
if os.path.exists(os.path.join(anno_dirname, 'hg19.gerp.bw')):
annos['gerp_bp'] = os.path.join(anno_dirname, 'hg19.gerp.bw')
if os.path.exists(
os.path.join(anno_dirname, 'whole_genome_SNVs.tsv.compressed.gz')):
annos['cadd_score'] = os.path.join(
anno_dirname, 'whole_genome_SNVs.tsv.compressed.gz')
return annos
