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import utility.logger
logger = utility.logger.getLogger(__name__ )
class genotype(object):
"""
Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
"""
def __init__(self, filename):
self.group = None
self.type = "riset"
self.prgy = []
self.nprgy = 0
self.mat = -1
self.pat = 1
self.het = 0
self.unk = "U"
self.filler = False
self.mb_exists = False
#ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary
self.cm_column = 2
self.mb_column = 3
self.chromosomes = []
self.read_file(filename)
def __iter__(self):
return iter(self.chromosomes)
def __getitem__(self, index):
return self.chromosomes[index]
def __len__(self):
return len(self.chromosomes)
def read_rdata_output(self, qtl_results):
#ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results
self.chromosomes = [] #ZS: Overwriting since the .geno file's contents are just placeholders
this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers
chr_ob = None
for marker in qtl_results:
locus = Locus(self)
if (str(marker['chr']) != this_chr) and this_chr != "X": #ZS: This is really awkward but works as a temporary fix
if this_chr != "":
self.chromosomes.append(chr_ob)
this_chr = str(marker['chr'])
if this_chr == "20":
this_chr = "X"
chr_ob = Chr(this_chr, self)
if 'chr' in marker:
locus.chr = str(marker['chr'])
if 'name' in marker:
locus.name = marker['name']
if 'Mb' in marker:
locus.Mb = marker['Mb']
if 'cM' in marker:
locus.cM = marker['cM']
chr_ob.loci.append(locus)
self.chromosomes.append(chr_ob)
return self
def read_file(self, filename):
with open(filename, 'r') as geno_file:
lines = geno_file.readlines()
this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers
chr_ob = None
for line in lines:
if line[0] == "#":
continue
elif line[0] == "@":
label = line.split(":")[0][1:]
if label == "name":
self.group = line.split(":")[1].strip()
elif label == "filler":
if line.split(":")[1].strip() == "yes":
self.filler = True
elif label == "type":
self.type = line.split(":")[1].strip()
elif label == "mat":
self.mat = line.split(":")[1].strip()
elif label == "pat":
self.pat = line.split(":")[1].strip()
elif label == "het":
self.het = line.split(":")[1].strip()
elif label == "unk":
self.unk = line.split(":")[1].strip()
else:
continue
elif line[:3] == "Chr":
header_row = line.split("\t")
if header_row[2] == "Mb":
self.mb_exists = True
self.mb_column = 2
self.cm_column = 3
elif header_row[3] == "Mb":
self.mb_exists = True
self.mb_column = 3
elif header_row[2] == "cM":
self.cm_column = 2
if self.mb_exists:
self.prgy = header_row[4:]
else:
self.prgy = header_row[3:]
self.nprgy = len(self.prgy)
else:
if line.split("\t")[0] != this_chr:
if this_chr != "":
self.chromosomes.append(chr_ob)
this_chr = line.split("\t")[0]
chr_ob = Chr(line.split("\t")[0], self)
chr_ob.add_marker(line.split("\t"))
self.chromosomes.append(chr_ob)
class Chr(object):
def __init__(self, name, geno_ob):
self.name = name
self.loci = []
self.mb_exists = geno_ob.mb_exists
self.cm_column = geno_ob.cm_column
self.mb_column = geno_ob.mb_column
self.geno_ob = geno_ob
def __iter__(self):
return iter(self.loci)
def __getitem__(self, index):
return self.loci[index]
def __len__(self):
return len(self.loci)
def add_marker(self, marker_row):
self.loci.append(Locus(self.geno_ob, marker_row))
class Locus(object):
def __init__(self, geno_ob, marker_row = None):
self.chr = None
self.name = None
self.cM = None
self.Mb = None
self.genotype = []
if marker_row:
self.chr = marker_row[0]
self.name = marker_row[1]
try:
self.cM = float(marker_row[geno_ob.cm_column])
except:
self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0
try:
self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
except:
self.Mb = self.cM
geno_table = {
geno_ob.mat: -1,
geno_ob.pat: 1,
geno_ob.het: 0,
geno_ob.unk: "U"
}
self.genotype = []
if geno_ob.mb_exists:
start_pos = 4
else:
start_pos = 3
for allele in marker_row[start_pos:]:
if allele in list(geno_table.keys()):
self.genotype.append(geno_table[allele])
else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
self.genotype.append("U")
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