def __add__(self, other):
if hasattr(other, "seq") and hasattr(other.seq, "watson"):
other = _copy.deepcopy(other)
for f in other.features:
f.location = f.location + other.seq.ovhg
answer = Dseqrecord(_SeqRecord.__add__(self, other))
answer.n = min(self.n, other.n)
else:
answer = Dseqrecord(_SeqRecord.__add__(self, Dseqrecord(other)))
answer.n = self.n
return answer
def test_lcs():
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as BSeqRecord
from pydna.dseq import Dseq
from pydna.dseqrecord import Dseqrecord
from pydna.seqrecord import SeqRecord
from pydna.seqfeature import SeqFeature
from Bio.SeqFeature import FeatureLocation, ExactPosition
s = SeqRecord(Seq("GGATCC"))
expected = SeqFeature()
expected.__dict__ = {
"location": FeatureLocation(ExactPosition(0),
ExactPosition(6),
strand=1),
"type": "read",
"id": "<unknown id>",
"qualifiers": {
"label": ["sequence"],
"ApEinfo_fwdcolor": ["#DAFFCF"],
"ApEinfo_revcolor": ["#DFFDFF"],
},
}
assert s.lcs("GGATCC", limit=4).__dict__ == expected.__dict__
assert s.lcs(Seq("GGATCC"), limit=4).__dict__ == expected.__dict__
assert (s.lcs(BSeqRecord(Seq("GGATCC"), name="sequence"),
limit=4).__dict__ == expected.__dict__)
assert s.lcs(Dseq("GGATCC"), limit=4).__dict__ == expected.__dict__
assert (s.lcs(Dseqrecord(Dseq("GGATCC"), name="sequence"),
limit=4).__dict__ == expected.__dict__)
assert (s.lcs(Dseqrecord("GGATCC", name="sequence"),
limit=4).__dict__ == expected.__dict__)
def test_format():
from Bio.Seq import Seq
from pydna.seqrecord import SeqRecord
s = SeqRecord(Seq("GGATCC"))
s.format("gb")
s.format("genbank")
s.format("fasta")
def test_format():
from Bio.Seq import Seq
from pydna.seqrecord import SeqRecord
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
s = SeqRecord(Seq("GGATCC",alphabet=IUPACAmbiguousDNA()))
s.format("gb")
s.format("genbank")
s.format("fasta")
def __add__(self, other):
if hasattr(other, "seq") and hasattr(other.seq, "watson"):
other = _copy.deepcopy(other)
other_five_prime = other.seq.five_prime_end()
if other_five_prime[0] == "5'":
# add other.seq.ovhg
for f in other.features:
f.location = f.location + other.seq.ovhg
elif other_five_prime[0] == "3'":
# subtract other.seq.ovhg (sign change)
for f in other.features:
f.location = f.location + (-other.seq.ovhg)
answer = Dseqrecord(_SeqRecord.__add__(self, other))
answer.n = min(self.n, other.n)
else:
answer = Dseqrecord(_SeqRecord.__add__(self, Dseqrecord(other)))
answer.n = self.n
return answer
def test___hash__():
from Bio.Seq import Seq
from pydna.seqrecord import SeqRecord
s = SeqRecord(Seq("GGATCC"))
t = SeqRecord(Seq("GGATCC"))
u = SeqRecord(Seq("GGATCc"))
assert hash(s) == hash(t) != hash(u)
assert s == t
assert s != u
assert s != "1"
assert s < u
assert not s > u
with pytest.raises(TypeError):
s > "3"
with pytest.raises(TypeError):
s < "3"
def test___hash__():
from Bio.Seq import Seq
from pydna.seqrecord import SeqRecord
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
s = SeqRecord(Seq("GGATCC",alphabet=IUPACAmbiguousDNA()))
t = SeqRecord(Seq("GGATCC",alphabet=IUPACAmbiguousDNA()))
u = SeqRecord(Seq("GGATCc",alphabet=IUPACAmbiguousDNA()))
assert hash(s) == hash(t) != hash(u)
assert s==t
assert s!=u
assert s!="1"
assert s<u
assert not s>u
with pytest.raises(TypeError):
s>"3"
with pytest.raises(TypeError):
s<"3"
def test_amplicon():
from pydna.amplify import Anneal
from pydna.dseqrecord import Dseqrecord
from pydna.primer import Primer
template = Dseqrecord("AAAtacactcaccgtctatcattatctactatcgactgtatcatctgatagcacTTT")
p1 = Primer("CCCtacactcaccgtctatcattatc")
p2 = Primer("GGGgtgctatcagatgatacagtcg")
ann = Anneal((p1,p2),template)
prod = ann.products[0]
assert repr(prod) == 'Amplicon(57)'
assert prod._repr_html_() == 'Amplicon(57)'
from unittest.mock import MagicMock
pp = MagicMock()
prod._repr_pretty_(pp, None)
#assert pp.text.assert_called_with('Amplicon(57)')
fig=''' 5tacactcaccgtctatcattatc...cgactgtatcatctgatagcac3
|||||||||||||||||||||| tm 55.9 (dbd) 60.5
3gctgacatagtagactatcgtgGGG5
5CCCtacactcaccgtctatcattatc3
||||||||||||||||||||||| tm 54.6 (dbd) 58.8
3atgtgagtggcagatagtaatag...gctgacatagtagactatcgtg5'''
import textwrap
assert prod.figure() == textwrap.dedent(fig)
assert prod.program() == prod.taq_program()
assert prod.pfu_sso7d_program() == prod.dbd_program()
from pydna.amplicon import Amplicon
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from pydna.seqrecord import SeqRecord
arg = SeqRecord(Seq("aaa", IUPACAmbiguousDNA()))
x = Amplicon.from_SeqRecord(arg)
def test_olaps():
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as BSeqRecord
from pydna.dseq import Dseq
from pydna.dseqrecord import Dseqrecord
from pydna.seqrecord import SeqRecord
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
s = SeqRecord(Seq("GGATCC",alphabet=IUPACAmbiguousDNA()))
assert "GGATCC" == str(s.olaps("GGATCC", limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Seq("GGATCC",alphabet=IUPACAmbiguousDNA()), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(BSeqRecord(Seq("GGATCC",alphabet=IUPACAmbiguousDNA())), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Dseq("GGATCC",alphabet=IUPACAmbiguousDNA()), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Dseqrecord(Dseq("GGATCC")), limit = 4)[0].seq)
assert "GGATCC" == str(s.olaps(Dseqrecord("GGATCC"), limit = 4)[0].seq)
def test_genbankfile():
from pydna import genbankrecord
gbr = genbankrecord.GenbankRecord("aaa")
assert (
gbr.hyperlink ==
"<a href='https://www.ncbi.nlm.nih.gov/nuccore/accession?from=&to=&strand=1' target='_blank'>accession</a>"
)
assert repr(gbr) == "Gbank(accession)(-3)"
assert (
gbr._repr_html_() ==
"<a href='https://www.ncbi.nlm.nih.gov/nuccore/accession?from=&to=&strand=1' target='_blank'>accession</a>"
)
from unittest.mock import MagicMock
pp = MagicMock()
gbr._repr_pretty_(pp, None)
pp.text.assert_called_with("Gbank(accession)(-3)")
gbr = genbankrecord.GenbankRecord("aaa", start=1, stop=2)
assert (
gbr.hyperlink ==
"<a href='https://www.ncbi.nlm.nih.gov/nuccore/accession?from=1&to=2&strand=1' target='_blank'>accession 1-2</a>"
)
gbr_rc = gbr.rc()
assert gbr_rc.strand == 2
from Bio.Seq import Seq
from pydna.seqrecord import SeqRecord
arg = SeqRecord(Seq("aaa"))
genbankrecord.GenbankRecord.from_SeqRecord(arg)
def __str__(self):
return ("Dseqrecord\n"
"circular: {}\n"
"size: {}\n").format(self.circular,
len(self)) + _SeqRecord.__str__(self)
def test_stamp():
from pydna.seqrecord import SeqRecord
from pydna.readers import read
from pydna.utils import eq
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as Srec
a = SeqRecord("attt")
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
assert "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo" in a.definition
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
a = SeqRecord("attt")
a.description = "something"
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
assert "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo" in a.definition
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
assert "something" in a.definition
a = SeqRecord("attt")
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
a.seq = a.seq + "a"
with pytest.raises(ValueError):
a.stamp()
a = SeqRecord(Seq("attt"))
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
assert "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo" in a.definition
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
a = SeqRecord(Seq("attt"))
a.description = "something"
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
assert "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo" in a.definition
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
assert "something" in a.definition
a = SeqRecord(Seq("attt"))
assert a.stamp() == "SEGUID_ot6JPLeAeMmfztW1736Kc6DAqlo"
a.seq = a.seq + "a"
with pytest.raises(ValueError):
a.stamp()
def test_add_feature():
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord as BSeqRecord
from pydna.dseq import Dseq
from pydna.dseqrecord import Dseqrecord
from pydna.seqrecord import SeqRecord
s = SeqRecord("tttGGATCCaaa")
s.add_feature(3, 9)
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq="GGATCC")
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=Seq("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=Dseq("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=SeqRecord("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=BSeqRecord("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
s.add_feature(seq=Dseqrecord("GGATCC"))
assert s.extract_feature(0).seq == SeqRecord("GGATCC").seq
s = SeqRecord("tttGGATCCaaa")
with pytest.raises(TypeError):
s.add_feature(seq=Dseqrecord("GGGGGG"))
s = SeqRecord("tttATGaaaTAAggg")
s.add_feature(3, 12)
assert s.features[0].qualifiers["label"] == ["orf9"]
from Bio.Seq import Seq
from pydna.seqrecord import SeqRecord
a = SeqRecord(Seq("atgtaa"))
a.add_feature(2, 4)
assert (
a.list_features() ==
"+-----+---------------+-----+-----+-----+-----+------+------+\n| Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |\n+-----+---------------+-----+-----+-----+-----+------+------+\n| 0 | L:ft2 | --> | 2 | 4 | 2 | misc | no |\n+-----+---------------+-----+-----+-----+-----+------+------+"
)
a.features[0].qualifiers
del a.features[0].qualifiers["label"]
assert (
a.list_features() ==
"+-----+---------------+-----+-----+-----+-----+------+------+\n| Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |\n+-----+---------------+-----+-----+-----+-----+------+------+\n| 0 | nd | --> | 2 | 4 | 2 | misc | no |\n+-----+---------------+-----+-----+-----+-----+------+------+"
)
a.features[0].qualifiers["note"] = ["AwesomeFeature"]
assert (
a.list_features() ==
"+-----+------------------+-----+-----+-----+-----+------+------+\n| Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |\n+-----+------------------+-----+-----+-----+-----+------+------+\n| 0 | N:AwesomeFeature | --> | 2 | 4 | 2 | misc | no |\n+-----+------------------+-----+-----+-----+-----+------+------+"
)
def test_contig(monkeypatch):
monkeypatch.setenv("pydna_cached_funcs", "")
from pydna import contig
from pydna.assembly import Assembly
from pydna.dseqrecord import Dseqrecord
a = Dseqrecord("acgatgctatactgCCCCCtgtgctgtgctcta", name="one")
b = Dseqrecord("tgtgctgtgctctaTTTTTtattctggctgtatc", name="two")
c = Dseqrecord("tattctggctgtatcGGGGGtacgatgctatactg", name="three")
asm = Assembly((a, b, c), limit=14)
cnt = asm.assemble_circular()[0]
assert repr(cnt) == "Contig(o59)"
assert cnt.detailed_figure() == str(
"||||||||||||||\n"
"acgatgctatactgCCCCCtgtgctgtgctcta\n"
" TGTGCTGTGCTCTA\n"
" tgtgctgtgctctaTTTTTtattctggctgtatc\n"
" TATTCTGGCTGTATC\n"
" tattctggctgtatcGGGGGtacgatgctatactg\n"
" ACGATGCTATACTG\n"
)
from textwrap import indent
fig = """ -|one|14
| \\/
| /\\
| 14|two|15
| \\/
| /\\
| 15|three|14
| \\/
| /\\
| 14-
| |
-------------------------"""
cnt2 = asm.assemble_linear()[0]
fig = ('one|14\n'
' \\/\n'
' /\\\n'
' 14|two|15\n'
' \\/\n'
' /\\\n'
' 15|three')
assert fig == cnt2.figure()
assert repr(cnt2) == 'Contig(-73)'
#print(repr(cnt2._repr_html_()))
assert cnt2._repr_html_(
) == '<pre>one|14\n \\/\n /\\\n 14|two|15\n \\/\n /\\\n 15|three</pre>'
from unittest.mock import MagicMock
pp = MagicMock()
cnt2._repr_pretty_(pp, None)
pp.text.assert_called_with('Contig(-73)')
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from pydna.seqrecord import SeqRecord
arg = SeqRecord(Seq("aaa", IUPACAmbiguousDNA()))
import networkx as nx
x = contig.Contig.from_SeqRecord(arg, graph=nx.MultiDiGraph())