def load(self):
#print "INFO: Loading dosage files"
#logging.info("Loading %s dosage", self.path)
class PrediXcanCollector(object):
def __init__(self, snps=[], snps_by_rsid={}, weight_db_logic=None):
self.snps = snps
self.snps_by_rsid = snps_by_rsid
self.weight_db_logic = weight_db_logic
def __call__(self, i, components):
rsid = components[PDTF.RSID]
if self.weight_db_logic and not rsid in self.weight_db_logic.genes_for_an_rsid:
logging.log(5, "rsid %s not in weight db, skip it", rsid)
return
position = components[PDTF.POSITION]
ref_allele = components[PDTF.ALLELE_0]
if not ref_allele in Utilities.VALID_ALLELES:
logging.log(9, "wrong ref allele, rsid %s is not an SNP", rsid)
return
eff_allele = components[PDTF.ALLELE_1]
if not eff_allele in Utilities.VALID_ALLELES:
logging.log(9, "wrong eff allele, rsid %s is not an SNP", rsid)
return
dosages = map(float,components[PDTF.FIRST_DATA_COLUMN:]) #dosages may be inputed
#Should we flip based on weight_db at this point?
snp = DataSetSNP.DataSetSNP(name=rsid, index=i, data=dosages, position=int(position), ref_allele=ref_allele, eff_allele=eff_allele)
if snp.name in self.snps_by_rsid:
old = self.snps_by_rsid[snp.name]
logging.info("Duplicated rsid: (%s,%s) %s", old.name, old.position, " ".join(components))
self.snps.append(snp)
self.snps_by_rsid[snp.name] = snp
loader = Utilities.CSVFileIterator(self.path, compressed=True)
collector = PrediXcanCollector(weight_db_logic=self.weight_db_logic)
loader.iterate(collector)
return collector.snps, collector.snps_by_rsid
def testCSVFileIterator(self):
class DummyCallback():
def __init__(self):
self.lines = []
def __call__(self, i, row):
self.lines.append((i, row))
c = DummyCallback()
f = Utilities.CSVFileIterator("tests/_td/dosage_set_1/set.sample",
header="a")
with self.assertRaises(Exceptions.MalformedInputFile):
f.iterate(c)
c = DummyCallback()
f = Utilities.CSVFileIterator("tests/_td/dosage_set_1/set.sample")
f.iterate(c)
self.assertEqual(c.lines, [(0, ["ID", "POP", "GROUP", "SEX"]),
(1, ["ID1", "K", "HERO", "male"]),
(2, ["ID2", "K", "HERO", "female"]),
(3, ["DI5", "K", "HERO", "male"]),
(4, ["ID3", "K", "HERO", "female"]),
(5, ["B1", "L", "T", "female"])])
c = DummyCallback()
f = Utilities.CSVFileIterator("tests/_td/dosage_set_1/set.sample", "")
f.iterate(c)
self.assertEqual(c.lines, [(0, ["ID1", "K", "HERO", "male"]),
(1, ["ID2", "K", "HERO", "female"]),
(2, ["DI5", "K", "HERO", "male"]),
(3, ["ID3", "K", "HERO", "female"]),
(4, ["B1", "L", "T", "female"])])
c = DummyCallback()
f = Utilities.CSVFileIterator("tests/_td/dosage_set_1/set.sample",
"DI5 K",
ignore_until_header=True)
f.iterate(c)
self.assertEqual(c.lines, [(0, ["ID3", "K", "HERO", "female"]),
(1, ["B1", "L", "T", "female"])])
c = DummyCallback()
f = Utilities.CSVFileIterator("tests/_td/dosage_set_1/set.sample",
header="ID POP GROUP SEX")
f.iterate(c)
self.assertEqual(c.lines, [(0, ["ID1", "K", "HERO", "male"]),
(1, ["ID2", "K", "HERO", "female"]),
(2, ["DI5", "K", "HERO", "male"]),
(3, ["ID3", "K", "HERO", "female"]),
(4, ["B1", "L", "T", "female"])])
c = DummyCallback()
f = Utilities.CSVFileIterator(
"tests/_td/dosage_set_1/set_chr1.legend.gz",
header="a",
compressed=True)
with self.assertRaises(Exceptions.MalformedInputFile):
f.iterate(c)
c = DummyCallback()
f = Utilities.CSVFileIterator(
"tests/_td/dosage_set_1/set_chr1.legend.gz", compressed=True)
f.iterate(c)
self.assertEqual(
c.lines,
[(0, [
"id", "position", "a0", "a1", "TYPE", "AFR", "AMR", "EAS",
"EUR", "SAS", "ALL"
]),
(1, [
"1:10177:A:AC", "10177", "A", "AC", "Biallelic_INDEL",
"0.490922844175492", "0.360230547550432", "0.336309523809524",
"0.405566600397614", "0.494887525562372", "0.425319488817891"
]),
(2, [
"rs1:1:A:T", "10505", "A", "T", "Biallelic_SNP", "0", "0",
"0", "0", "0", "0"
]),
(3, [
"1:12:C:G", "10506", "C", "G", "Biallelic_SNP", "0", "0", "0",
"0", "0", "0"
]),
(4, [
"rs2:2:G:A", "10511", "G", "A", "Biallelic_SNP", "0", "0",
"0", "0", "0", "0"
]),
(5, [
"rs3:3:C:T", "10511", "G", "A", "Biallelic_SNP", "0", "0",
"0", "0", "0", "0"
]),
(6, [
"rs4:4:C:T", "10511", "G", "A", "Biallelic_SNP", "0", "0",
"0", "0", "0", "0"
])])
c = DummyCallback()
f = Utilities.CSVFileIterator(
"tests/_td/dosage_set_1/set_chr1.legend.gz",
header="id position a0 a1 TYPE AFR AMR EAS EUR SAS ALL",
compressed=True)
f.iterate(c)
self.assertEqual(
c.lines, [(0, [
"1:10177:A:AC", "10177", "A", "AC", "Biallelic_INDEL",
"0.490922844175492", "0.360230547550432", "0.336309523809524",
"0.405566600397614", "0.494887525562372", "0.425319488817891"
]),
(1, [
"rs1:1:A:T", "10505", "A", "T", "Biallelic_SNP", "0",
"0", "0", "0", "0", "0"
]),
(2, [
"1:12:C:G", "10506", "C", "G", "Biallelic_SNP", "0",
"0", "0", "0", "0", "0"
]),
(3, [
"rs2:2:G:A", "10511", "G", "A", "Biallelic_SNP", "0",
"0", "0", "0", "0", "0"
]),
(4, [
"rs3:3:C:T", "10511", "G", "A", "Biallelic_SNP", "0",
"0", "0", "0", "0", "0"
]),
(5, [
"rs4:4:C:T", "10511", "G", "A", "Biallelic_SNP", "0",
"0", "0", "0", "0", "0"
])])
