def UniGeneParser(lines):
"""Treats lines as a stream of unigene records"""
for record in GbFinder(lines):
curr = LinesToUniGene(record)
del curr["//"] # clean up delimiter
yield curr
def test_LinesToUniGene(self):
"""LinesToUniGene should give expected results on sample data"""
fake_file = """ID Mm.1
TITLE S100 calcium binder
GENE S100a10
CYTOBAND 3 41.7 cM
LOCUSLINK 20194
EXPRESS embryo ; whole body ; mammary gland ; brain
CHROMOSOME 3
STS ACC=RH128467 UNISTS=211775
STS ACC=M16465 UNISTS= 178878
PROTSIM ORG=H**o sapiens; PROTGI=107251; PROTID=pir:JC1139; PCT=91; ALN=97
PROTSIM ORG=Mus musculus; PROTGI=116487; PROTID=sp:P08207; PCT=100; ALN=97
PROTSIM ORG=Rattus norvegicus; PROTGI=116489; PROTID=sp:P05943; PCT=94; ALN=94
SCOUNT 5
SEQUENCE ACC=BC025044.1; NID=g19263549; PID=g19263550; SEQTYPE=mRNA
SEQUENCE ACC=AA471893.1; NID=g2199884; CLONE=IMAGE:872193; END=5'; LID=539; SEQTYPE=EST
SEQUENCE ACC=AI842963.1; NID=g5477176; CLONE=UI-M-AO1-aem-f-10-0-UI; END=3'; LID=1944; SEQTYPE=EST; TRACE=158501677
SEQUENCE ACC=CB595147.1; NID=g29513003; CLONE=IMAGE:30300703; END=5'; LID=12885; MGC=6677832; SEQTYPE=EST
SEQUENCE ACC=BY144053.1; NID=g26280109; CLONE=L930184D22; END=5'; LID=12267; SEQTYPE=EST
//
ID Mm.5
TITLE homeo box A10
GENE Hoxa10
CYTOBAND 6 26.33 cM
LOCUSLINK 15395
EXPRESS kidney ; colon ; mammary gland
CHROMOSOME 6
PROTSIM ORG=Caenorhabditis elegans; PROTGI=7510074; PROTID=pir:T31611; PCT=30; ALN=326
SCOUNT 1
SEQUENCE ACC=AW990320.1; NID=g8185938; CLONE=IMAGE:1513482; END=5'; LID=1043; SEQTYPE=EST; TRACE=94472873
//
"""
records = list(GbFinder(fake_file.split("\n")))
self.assertEqual(len(records), 2)
first, second = list(map(LinesToUniGene, records))
self.assertEqual(first.ID, "Mm.1")
self.assertEqual(first.TITLE, "S100 calcium binder")
self.assertEqual(first.GENE, "S100a10")
self.assertEqual(first.CYTOBAND, "3 41.7 cM")
self.assertEqual(first.CHROMOSOME, "3")
self.assertEqual(first.LOCUSLINK, 20194)
self.assertEqual(first.EXPRESS,
["embryo", "whole body", "mammary gland", "brain"])
self.assertEqual(
first.STS,
[
{
"ACC": "RH128467",
"UNISTS": "211775"
},
{
"ACC": "M16465",
"UNISTS": "178878"
},
],
)
exp_prot_sim = list(
map(
UniGeneProtSimRecord,
[
{
"ORG": "H**o sapiens",
"PROTGI": "107251",
"PROTID": "pir:JC1139",
"PCT": "91",
"ALN": "97",
},
{
"ORG": "Mus musculus",
"PROTGI": "116487",
"PROTID": "sp:P08207",
"PCT": "100",
"ALN": "97",
},
{
"ORG": "Rattus norvegicus",
"PROTGI": "116489",
"PROTID": "sp:P05943",
"PCT": "94",
"ALN": "94",
},
],
))
for obs, exp in zip(first.PROTSIM, exp_prot_sim):
self.assertEqual(obs, exp)
self.assertEqual(first.SCOUNT, 5)
exp_seqs = list(
map(
UniGeneSeqRecord,
[
{
"ACC": "BC025044.1",
"NID": "g19263549",
"PID": "g19263550",
"SEQTYPE": "mRNA",
},
{
"ACC": "AA471893.1",
"NID": "g2199884",
"END": "5'",
"CLONE": "IMAGE:872193",
"LID": "539",
"SEQTYPE": "EST",
},
{
"ACC": "AI842963.1",
"NID": "g5477176",
"CLONE": "UI-M-AO1-aem-f-10-0-UI",
"END": "3'",
"LID": "1944",
"SEQTYPE": "EST",
"TRACE": "158501677",
},
{
"ACC": "CB595147.1",
"NID": "g29513003",
"CLONE": "IMAGE:30300703",
"END": "5'",
"LID": "12885",
"MGC": "6677832",
"SEQTYPE": "EST",
},
{
"ACC": "BY144053.1",
"NID": "g26280109",
"CLONE": "L930184D22",
"END": "5'",
"LID": "12267",
"SEQTYPE": "EST",
},
],
))
for obs, exp in zip(first.SEQUENCE, exp_seqs):
self.assertEqual(obs, exp)
self.assertEqual(second.ID, "Mm.5")
self.assertEqual(second.TITLE, "homeo box A10")
self.assertEqual(second.GENE, "Hoxa10")
self.assertEqual(second.CYTOBAND, "6 26.33 cM")
self.assertEqual(second.LOCUSLINK, 15395)
self.assertEqual(second.EXPRESS, ["kidney", "colon", "mammary gland"])
self.assertEqual(second.CHROMOSOME, "6")
self.assertEqual(
second.PROTSIM,
list(
map(
UniGeneProtSimRecord,
[{
"ORG": "Caenorhabditis elegans",
"PROTGI": "7510074",
"PROTID": "pir:T31611",
"PCT": "30",
"ALN": "326",
}],
)),
)
self.assertEqual(second.SCOUNT, 1)
self.assertEqual(second.STS, [])
self.assertEqual(
second.SEQUENCE,
list(
map(
UniGeneSeqRecord,
[{
"ACC": "AW990320.1",
"NID": "g8185938",
"CLONE": "IMAGE:1513482",
"END": "5'",
"LID": "1043",
"SEQTYPE": "EST",
"TRACE": "94472873",
}],
)),
)
# test that the synonym mapping works OK
self.assertEqual(second.SequenceIds[0].NucleotideId, "g8185938")