def get_actionable_mutations(parser, args):
t_n_pairs = gemini_subjects.get_families(args.db)
query = "SELECT variants.chrom, start, end, ref, alt, \
variants.gene, impact, is_somatic, \
gene_summary.in_cosmic_census \
FROM variants, gene_summary \
WHERE variants.is_somatic = 1 \
AND (variants.type = 'snp' \
OR variants.type = 'indel') \
AND (variants.impact_severity = 'HIGH' \
OR variants.impact_severity = 'MED') \
AND variants.chrom = gene_summary.chrom \
AND variants.gene = gene_summary.gene \
AND gene_summary.in_cosmic_census = 1"
# collect the relevant genes and query DGIDB
gq = GeminiQuery.GeminiQuery(args.db)
gq.run(query)
genes = defaultdict()
for row in gq:
genes[row['gene']] = True
# collect info from DGIdb
dgidb_info = query_dgidb(genes)
# now rerun the query and report actionable mutations per DGIDB and COSMIC census.
gq = GeminiQuery.GeminiQuery(args.db)
gq.run(query)
print('\t'.join(['tum_name', 'chrom', 'start', 'end', 'ref', 'alt', \
'gene', 'impact', 'is_somatic', 'in_cosmic_census',
'dgidb_info']))
for row in gq:
for pair in t_n_pairs:
samples = pair.subjects
if len(samples) != 2:
continue
tumor = pair.subjects[0]
normal = pair.subjects[1]
# swap if we guessed the tumor incorrectly
if tumor.affected is False:
tumor, normal = normal, tumor
print('\t'.join(str(s) for s in [tumor.name, row['chrom'], \
row['start'], row['end'], \
row['ref'], row['alt'], \
row['gene'], row['impact'], \
row['is_somatic'], \
row['in_cosmic_census'], \
str(dgidb_info[row['gene']])]))
def find_de_novo():
#defines input arguments
parser = argparse.ArgumentParser(description='Finds de novos')
parser.add_argument('-f','--input_file', default='', help='The input file; should be a SQLite .db that gemini can read')
parser.add_argument('-p','--min_total_parent_depth', default = '0', help='The minimum total read depth for parental alleles for variants to be considered')
parser.add_argument('-c','--min_total_child_depth', default = '0', help='The minimum total read depth for child alleles for variants to be considered')
parser.add_argument('-m','--max_alt_parent_depth', default = '0', help='The maximum alternate read depth for parental alleles for de novos to be considered')
parser.add_argument('-a','--max_alt_child_depth', default = '0', help='The maximum alternate read depth for child alleles for de novos to be considered')
#checks minimum number of arguments
if len(sys.argv)<1:
parser.print_help()
sys.exit("Where is the input file?")
#parses arguments
args = parser.parse_args()
database=args.input_file
mtpd=int(args.min_total_parent_depth)
mtcd=int(args.min_total_child_depth)
mapd=int(args.max_alt_parent_depth)
macd=int(args.max_alt_child_depth)
if database == '':
sys.exit("You must supply an input file")
gq=GeminiQuery(database)
families = subjects.get_families(database)
gq.run("select chrom, start, end, ref, alt, gene, impact, gts, gt_types, gt_ref_depths, gt_alt_depths from variants")
s2i=gq.sample_to_idx
for row in gq:
mendelian = ""
phasable = ""
inheritance = ""
origin = ""
phasedata = ""
chrom = str(row['chrom'])
start = str(row['start'])
end = str(row['end'])
ref = str(row['ref'])
alt = str(row['alt'])
gene = str(row['gene'])
impact = str(row['impact'])
for family in families:
dad_idx = s2i[family.father_name]
mom_idx = s2i[family.mother_name]
dad_gt = str(row['gts'][dad_idx])
mom_gt = str(row['gts'][mom_idx])
dad_gt_type = row['gt_types'][dad_idx]
mom_gt_type = row['gt_types'][mom_idx]
dad_gt_ref_depths = str(row['gt_ref_depths'][dad_idx])
mom_gt_ref_depths = str(row['gt_ref_depths'][mom_idx])
dad_gt_alt_depths = str(row['gt_alt_depths'][dad_idx])
mom_gt_alt_depths = str(row['gt_alt_depths'][mom_idx])
#m5=re.search('((?:\w*|\.*))/((?:\w*|\.*))',dad_gt)
m5=string.split(dad_gt,"/")
#m6=re.search('((?:\w*|\.*))/((?:\w*|\.*))',mom_gt)
m6=string.split(mom_gt,"/")
for child in family.children:
kid_idx = s2i[str(child.name)]
kid_gt = str(row['gts'][kid_idx])
kid_gt_type = row['gt_types'][kid_idx]
kid_gt_ref_depths = str(row['gt_ref_depths'][kid_idx])
kid_gt_alt_depths = str(row['gt_alt_depths'][kid_idx])
#code for removing variants that do not meet parameters
if int(dad_gt_ref_depths)+int(dad_gt_alt_depths)<mtpd or int(mom_gt_ref_depths)+int(mom_gt_alt_depths)<mtpd \
or int(kid_gt_ref_depths)+int(kid_gt_alt_depths)<mtcd \
or int(dad_gt_alt_depths)>mapd or int(mom_gt_alt_depths)>mapd \
or int(kid_gt_alt_depths)>macd: \
continue
if kid_gt_type == 2 or dad_gt_type == 2 or mom_gt_type == 2:
continue
elif kid_gt_type == 1 and dad_gt_type == 0 and mom_gt_type == 0 or kid_gt_type == 1 and dad_gt_type == 3 and mom_gt_type == 3:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
elif kid_gt_type == 0 and dad_gt_type == 3 and mom_gt_type == 3 or kid_gt_type == 3 and dad_gt_type == 0 and mom_gt_type == 0:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "extremely rare de novo or bad data"
elif kid_gt_type == 0 and dad_gt_type == 1 and mom_gt_type == 3 or kid_gt_type == 0 and dad_gt_type == 3 and mom_gt_type == 1 or kid_gt_type == 3 and dad_gt_type == 0 and mom_gt_type == 1 or kid_gt_type == 3 and dad_gt_type == 1 and mom_gt_type == 0:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
elif kid_gt_type == 3 and dad_gt_type == 3 and mom_gt_type == 0 or kid_gt_type == 0 and dad_gt_type == 0 and mom_gt_type == 3:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
elif kid_gt_type == 0 and dad_gt_type == 3 and mom_gt_type == 0 or kid_gt_type == 3 and dad_gt_type == 0 and mom_gt_type == 3:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
else:
continue
print chrom + " " + start + " " + end + " " + family.family_id + " " + child.name + " " + ref + " " + alt + " " + gene + " " + impact + " " + kid_gt_ref_depths + " " + dad_gt_ref_depths + " " + mom_gt_ref_depths + " " + kid_gt_alt_depths + " " + dad_gt_alt_depths + " " + mom_gt_alt_depths + " " + kid_gt + " " + dad_gt + " " + mom_gt + " " + str(kid_gt_type) + " " + str(dad_gt_type) + " " + str(mom_gt_type) + " " + mendelian + " " + phasable + " " + inheritance + " " + origin
def phase_genotypes(database):
gq=GeminiQuery(database)
families = subjects.get_families(database)
gq.run("select chrom, start, end, ref, alt, gene, impact, gts, gt_types, gt_ref_depths, gt_alt_depths from variants")
s2i=gq.sample_to_idx
for row in gq:
mendelian = ""
phasable = ""
inheritance = ""
origin = ""
phasedata = ""
chrom = str(row['chrom'])
start = str(row['start'])
end = str(row['end'])
ref = str(row['ref'])
alt = str(row['alt'])
gene = str(row['gene'])
impact = str(row['impact'])
for family in families:
dad_idx = s2i[family.father_name]
mom_idx = s2i[family.mother_name]
dad_gt = str(row['gts'][dad_idx])
mom_gt = str(row['gts'][mom_idx])
dad_gt_type = row['gt_types'][dad_idx]
mom_gt_type = row['gt_types'][mom_idx]
dad_gt_ref_depths = str(row['gt_ref_depths'][dad_idx])
mom_gt_ref_depths = str(row['gt_ref_depths'][mom_idx])
dad_gt_alt_depths = str(row['gt_alt_depths'][dad_idx])
mom_gt_alt_depths = str(row['gt_alt_depths'][mom_idx])
#m5=re.search('((?:\w*|\.*))/((?:\w*|\.*))',dad_gt)
m5=string.split(dad_gt,"/")
#m6=re.search('((?:\w*|\.*))/((?:\w*|\.*))',mom_gt)
m6=string.split(mom_gt,"/")
for child in family.children:
kid_idx = s2i[str(child.name)]
kid_gt = str(row['gts'][kid_idx])
kid_gt_type = row['gt_types'][kid_idx]
kid_gt_ref_depths = str(row['gt_ref_depths'][kid_idx])
kid_gt_alt_depths = str(row['gt_alt_depths'][kid_idx])
if kid_gt_type == 0 and dad_gt_type == 1 and mom_gt_type == 1 or kid_gt_type == 3 and dad_gt_type == 1 and mom_gt_type == 1:
mendelian = "mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "inherited from both parents"
elif kid_gt_type == 0 and dad_gt_type == 0 and mom_gt_type == 0 or kid_gt_type == 1 and dad_gt_type == 1 and mom_gt_type == 1 or kid_gt_type == 3 and dad_gt_type == 3 and mom_gt_type == 3:
mendelian = "mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "inherited from both parents"
elif kid_gt_type == 2 or dad_gt_type == 2 or mom_gt_type == 2:
mendelian = "missing allele - unknown"
phasable = "missing allele - unknown"
inheritance = "missing allele - unknown"
origin = "missing allele - unknown"
elif kid_gt_type == 1 and dad_gt_type == 0 and mom_gt_type == 0 or kid_gt_type == 1 and dad_gt_type == 3 and mom_gt_type == 3:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
elif kid_gt_type == 0 and dad_gt_type == 3 and mom_gt_type == 3 or kid_gt_type == 3 and dad_gt_type == 0 and mom_gt_type == 0:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "extremely rare de novo or bad data"
elif kid_gt_type == 0 and dad_gt_type == 0 and mom_gt_type == 1 or kid_gt_type == 0 and dad_gt_type == 1 and mom_gt_type == 0 or kid_gt_type == 3 and dad_gt_type == 3 and mom_gt_type == 1 or kid_gt_type == 3 and dad_gt_type == 1 and mom_gt_type == 3:
mendelian = "mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "inherited from both parents or unlikely de novo"
elif kid_gt_type == 1 and dad_gt_type == 3 and mom_gt_type == 1:
mendelian = "mendelian"
phasable = "phasable"
inheritance = "homozygous alternate from dad, heterozygous allele from mom"
origin = "inherited from both parents or unlikely de novo"
ct=0
if m5[0] == m6[ct]:
phasedata = m5[0]+" from dad "+m6[ct+1]+" from mom"
else:
phasedata = m5[0]+" from dad "+m6[ct]+" from mom"
elif kid_gt_type == 1 and dad_gt_type == 0 and mom_gt_type == 1:
mendelian = "mendelian"
phasable = "phasable"
inheritance = "homozygous reference from dad_gt_type, heterozygous allele from mom_gt_type"
origin = "inherited from both parents or unlikely de novo"
ct=0
if m5[0] == m6[ct]:
phasedata = m5[0]+" from dad "+m6[ct+1]+" from mom"
else:
phasedata = m5[0]+" from dad "+m6[ct]+" from mom"
elif kid_gt_type == 1 and dad_gt_type == 1 and mom_gt_type == 3:
mendelian = "mendelian"
phasable = "phasable"
inheritance = "heterozygous allele from dad_gt_type, homozygous alternate from mom_gt_type"
origin = "inherited from both parents or unlikely de novo"
ct=0
if m5[ct] == m6[0]:
phasedata = m5[ct+1]+" from dad "+m6[0]+" from mom"
else:
phasedata = m5[ct]+" from dad "+m6[0]+" from mom"
elif kid_gt_type == 1 and dad_gt_type == 1 and mom_gt_type == 0:
mendelian = "mendelian"
phasable = "phasable"
inheritance = "heterozygous allele from dad_gt_type, homozygous reference from mom_gt_type"
origin = "inherited from both parents or unlikely de novo"
ct=0
if m5[ct] == m6[0]:
phasedata = m5[ct+1]+" from dad "+m6[0]+" from mom"
else:
phasedata = m5[ct]+" from dad "+m6[0]+" from mom"
elif kid_gt_type == 0 and dad_gt_type == 1 and mom_gt_type == 3 or kid_gt_type == 0 and dad_gt_type == 3 and mom_gt_type == 1 or kid_gt_type == 3 and dad_gt_type == 0 and mom_gt_type == 1 or kid_gt_type == 3 and dad_gt_type == 1 and mom_gt_type == 0:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
elif kid_gt_type == 3 and dad_gt_type == 3 and mom_gt_type == 0 or kid_gt_type == 0 and dad_gt_type == 0 and mom_gt_type == 3:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
elif kid_gt_type == 1 and dad_gt_type == 3 and mom_gt_type == 0:
mendelian = "mendelian"
phasable = "phasable"
inheritance = "homozygous alternate from dad_gt_type, homozygous reference from mom_gt_type"
origin = "inherited from both parents or unlikely de novo"
phasedata = m5[0]+" from dad "+m6[0]+" from mom"
elif kid_gt_type == 1 and dad_gt_type == 0 and mom_gt_type == 3:
mendelian = "mendelian"
phasable = "phasable"
inheritance = "homozygous reference from dad_gt_type, homozygous alternate from mom_gt_type"
origin = "inherited from both parents or unlikely de novo"
phasedata = m5[0]+" from dad "+m6[0]+" from mom"
elif kid_gt_type == 0 and dad_gt_type == 3 and mom_gt_type == 0 or kid_gt_type == 3 and dad_gt_type == 0 and mom_gt_type == 3:
mendelian = "non-mendelian"
phasable = "unphasable"
inheritance = "unknown"
origin = "de novo or erroneous data"
try:
print chrom + " " + start + " " + end + " " + family.family_id + " " + child.name + " " + ref + " " + alt + " " + gene + " " + impact + " " + kid_gt_ref_depths + " " + dad_gt_ref_depths + " " + mom_gt_ref_depths + " " + kid_gt_alt_depths + " " + dad_gt_alt_depths + " " + mom_gt_alt_depths + " " + kid_gt + " " + dad_gt + " " + mom_gt + " " + str(kid_gt_type) + " " + str(dad_gt_type) + " " + str(mom_gt_type) + " " + mendelian + " " + phasable + " " + inheritance + " " + origin + " " + phasedata
except TypeError:
print chrom + " " + start + " " + end + " " + family.family_id + " " + child.name + " " + ref + " " + alt + " " + gene + " " + impact + " " + kid_gt_ref_depths + " " + dad_gt_ref_depths + " " + mom_gt_ref_depths + " " + kid_gt_alt_depths + " " + dad_gt_alt_depths + " " + mom_gt_alt_depths + " " + kid_gt + " " + dad_gt + " " + mom_gt + " " + str(kid_gt_type) + " " + str(dad_gt_type) + " " + str(mom_gt_type) + " " + mendelian + " " + phasable + " " + inheritance + " " + origin