"RNAi": '3',
"AMP": '4',
"signalling": '5',
}
# load results from HelPopGen run
with open("../results/results_thres0.1_150615052013.csv", 'r') as f:
field_names = f.readline().rstrip().split(',')
rows = [x for x in csv.DictReader(f, fieldnames=field_names)]
# load list of immunity genes
with open("../data/ImmunityGenes2.csv", 'r') as f:
field_names = f.readline().rstrip().split(',')
immunity_genes = [x for x in csv.DictReader(f, fieldnames=field_names)]
mapped_immunity_genes = mapped([x['Hmel_ID'] for x in immunity_genes])
control_genes = getControlGenes(mapped_immunity_genes)
def writeMKtestInputFile(FILE, lines):
with open(FILE, 'w') as f:
f.writelines([','.join([line['D_N'],
line['NSsites'],
line['in_P_N'],
line['NSsites'],
line['D_S'],
line['Ssites'],
line['in_P_S'],
line['Ssites'],
line['ingroup_sequences'],
'0', # chr
from controlGenes import getControlGenes, mapped
# immunity genes by class
classes = {"humoral_recognition": "1", "cellular_recognition": "2", "RNAi": "3", "AMP": "4", "signaling": "5"}
# load results from HelPopGen run
with open("../results/results_thres0.1_150615052013.csv", "r") as f:
field_names = f.readline().rstrip().split(",")
rows = [x for x in csv.DictReader(f, fieldnames=field_names)]
# load list of immunity genes
with open("../data/hmel_dmel_orthologues.csv", "r") as f:
field_names = f.readline().rstrip().split(",")
immunity_genes = [x for x in csv.DictReader(f, fieldnames=field_names)]
mapped_immunity_genes = mapped([x["Hmel_ID"] for x in immunity_genes])
control_genes = getControlGenes(mapped_immunity_genes)
# load Obbard 2009 gene table
with open("../data/s027_all.csv", "r") as f:
field_names = f.readline().rstrip().split(",")
Obb_genes = [x for x in csv.DictReader(f, fieldnames=field_names)]
# get classes
for i in immunity_genes:
d = i["Dmel_ID"]
for g in Obb_genes:
if g["FBgn"] == d:
i["Class"] = g["Class"]
i["Cell_Hum"] = g["Cell_Hum"]
#
# Load completer list of immunity genes
#
with open("../data/immunity_genes.csv", "r") as f:
imm = [x.rstrip().split(",") for x in f.readlines()]
###
#
# Produce lists of data for mapped genes with orthologues
#
dmel_ids = [x["FBgn"] for x in obb]
hmel_ids = [x["locus"] for x in hpg]
mapped_hmel_ids = mapped(hmel_ids)
orthologues_with_data = [x for x in orthologues if x["Dmel_ID"] in dmel_ids and x["Hmel_ID"] in mapped_hmel_ids]
dmel_ids_with_orthologues = list()
for o in orthologues_with_data:
for l in obb:
if o["Dmel_ID"] == l["FBgn"]:
dmel_ids_with_orthologues.append(dict(l)) # use dict explicitly to force deep copy
hmel_ids_with_orthologues = list()
for o in orthologues_with_data:
for l in hpg:
if o["Hmel_ID"] == l["locus"]:
hmel_ids_with_orthologues.append(dict(l)) # use dict explicitly to force deep copy
# control_gene_names = getControlGenes([x['locus'] for x in hmel_ids_with_orthologues], 20)
control_gene_names = getControlGenes([y[0] for y in imm], 10)
control_genes = [x for x in hpg if x["locus"] in control_gene_names]
immunity_genes = [x for x in hpg if x["locus"] in [y[0] for y in imm]]
