def test_download():
a = pydna.Genbank("*****@*****.**")
v = os.environ["pydna_cache"]
os.environ["pydna_cache"] = "nocache"
gb = pydna.Genbank("*****@*****.**")
result = gb.nucleotide("L09137")
assert len(result) == 2686
assert seguid(result.seq) == "71B4PwSgBZ3htFjJXwHPxtUIPYE"
os.environ["pydna_cache"] = v
def test_download():
a = pydna.Genbank("*****@*****.**")
v = os.environ["pydna_cache"]
os.environ["pydna_cache"] = "nocache"
gb = pydna.Genbank("*****@*****.**")
result = gb.nucleotide("L09137")
assert len(result) == 2686
assert seguid(result.seq) == "71B4PwSgBZ3htFjJXwHPxtUIPYE"
os.environ["pydna_cache"] = v
def test_copy_features(self):
from pydna.utils import seguid
from pydna import read,copy_features
a=read("./pCAPs.gb")
b=read("./pCAPs_fasta.txt")
for sh in [1,2,3,3127,3128,3129]:
newb = (b[sh:]+b[:sh]).looped()
copy_features(a, newb)
#print "a",[len(str(f.extract(a).seq.lower()) for f in a.features if len(f)>10]
#print "b",[len(str(f.extract(newb).seq).lower()) for f in newb.features]
self.assertTrue( sorted([str(f.extract(a).seq).lower() for f in a.features if len(f)>10],key=len)
== sorted([str(f.extract(newb).seq).lower() for f in newb.features],key=len))
b=b.rc()
for sh in [1,2,3,3127,3128,3129]:
newb = b[sh:]+b[:sh]
copy_features(a, newb)
self.assertTrue( sorted([str(f.extract(a).seq).lower() for f in a.features if len(f)>10],key=len) == sorted([str(f.extract(newb).seq).lower() for f in newb.features],key=len))
seguid_bla = "riT98j2v4NxVS8sbw_Q8epCwQwo"
seguid_cre = "xLZ2xs2O8CUMmWh2OrhmNFp5ZLg"
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("attaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("ttaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("taacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("gttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("ttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,seguid_bla,seguid_bla]
b=read("./pCAPs_fasta.txt").looped()
b=b.synced("taccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [seguid_cre,seguid_cre,]
def test_copy_features(self):
from pydna.utils import seguid
from pydna import read, copy_features
a = read("./pCAPs.gb")
b = read("./pCAPs_fasta.txt")
for sh in [1, 2, 3, 3127, 3128, 3129]:
newb = (b[sh:] + b[:sh]).looped()
copy_features(a, newb)
#print "a",[len(str(f.extract(a).seq.lower()) for f in a.features if len(f)>10]
#print "b",[len(str(f.extract(newb).seq).lower()) for f in newb.features]
self.assertTrue(
sorted([
str(f.extract(a).seq).lower()
for f in a.features if len(f) > 10
],
key=len) ==
sorted(
[str(f.extract(newb).seq).lower() for f in newb.features],
key=len))
b = b.rc()
for sh in [1, 2, 3, 3127, 3128, 3129]:
newb = b[sh:] + b[:sh]
copy_features(a, newb)
self.assertTrue(
sorted([
str(f.extract(a).seq).lower()
for f in a.features if len(f) > 10
],
key=len) ==
sorted(
[str(f.extract(newb).seq).lower() for f in newb.features],
key=len))
seguid_bla = "riT98j2v4NxVS8sbw_Q8epCwQwo"
seguid_cre = "xLZ2xs2O8CUMmWh2OrhmNFp5ZLg"
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("attaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("ttaacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("taacgagtgccgtaaacgacgatggttttacc")
copy_features(a, b)
assert [seguid(f.extract(b).seq)
for f in b.features] == [seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("gttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("ttaccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features
] == [seguid_cre, seguid_cre, seguid_bla, seguid_bla]
b = read("./pCAPs_fasta.txt").looped()
b = b.synced("taccaatgcttaatcagtgaggcacctatctcagc")
copy_features(a, b)
assert [seguid(f.extract(b).seq) for f in b.features] == [
seguid_cre,
seguid_cre,
]