def test_repr_pretty_():
from pydna._pretty import pretty_str
from unittest.mock import MagicMock
pp = MagicMock()
s = pretty_str("123")
t = s._repr_pretty_(pp, None)
pp.text.assert_called_with("123")
def small_fig(self):
'''
Returns a small ascii representation of the assembled fragments. Each fragment is
represented by:
::
Size of common 5' substring|Name and size of DNA fragment| Size of common 5' substring
Linear:
::
frag20| 6
\\/
/\\
6|frag23| 6
\\/
/\\
6|frag14
Circular:
::
-|2577|61
| \\/
| /\\
| 61|5681|98
| \\/
| /\\
| 98|2389|557
| \\/
| /\\
| 557-
| |
--------------------------
'''
if self.linear:
'''
frag20| 6
\/
/\
6|frag23| 6
\/
/\
6|frag14
'''
f = self.source_fragments[0]
space2 = len(f.name)
fig = ("{name}|{o2:>2}\n"
"{space2} \/\n"
"{space2} /\\\n").format(name = f.name,
o2 = f.right_overlap_size,
space2 = " "*space2)
space = len(f.name)
for f in self.source_fragments[1:-1]:
name= "{o1:>2}|{name}|".format(o1 = f.left_overlap_size,
name = f.name)
space2 = len(name)
fig +=("{space} {name}{o2:>2}\n"
"{space} {space2}\/\n"
"{space} {space2}/\\\n").format( name = name,
o2 = f.right_overlap_size,
space = " "*space,
space2 = " "*space2)
space +=space2
f = self.source_fragments[-1]
fig += ("{space} {o1:>2}|{name}").format(name = f.name,
o1 = f.left_overlap_size,
space = " "*(space))
else:
'''
-|2577|61
| \/
| /\
| 61|5681|98
| \/
| /\
| 98|2389|557
| \/
| /\
| 557-
| |
--------------------------
'''
f = self.source_fragments[0]
space = len(f.name)+3
fig =(" -|{name}|{o2:>2}\n"
"|{space}\/\n"
"|{space}/\\\n").format(name = f.name,
o2 = f.right_overlap_size,
space = " "*space)
for f in self.source_fragments[1:]:
name= "{o1:>2}|{name}|".format(o1 = f.left_overlap_size,
name = f.name)
space2 = len(name)
fig +=("|{space}{name}{o2:>2}\n"
"|{space}{space2}\/\n"
"|{space}{space2}/\\\n").format(o2 = f.right_overlap_size,
name = name,
space = " "*space,
space2 = " "*space2)
space +=space2
fig +="|{space}{o1:>2}-\n".format(space=" "*(space), o1=self.source_fragments[0].left_overlap_size)
fig +="|{space} |\n".format(space=" "*(space))
fig +=" {space}".format(space="-"*(space+3))
return pretty_str(dedent(fig))
def small_fig(self):
'''
Returns a small ascii representation of the assembled fragments. Each fragment is
represented by:
::
Size of common 5' substring|Name and size of DNA fragment| Size of common 5' substring
Linear:
::
frag20| 6
\\/
/\\
6|frag23| 6
\\/
/\\
6|frag14
Circular:
::
-|2577|61
| \\/
| /\\
| 61|5681|98
| \\/
| /\\
| 98|2389|557
| \\/
| /\\
| 557-
| |
--------------------------
'''
if self.linear:
'''
frag20| 6
\/
/\
6|frag23| 6
\/
/\
6|frag14
'''
f = self.source_fragments[0]
space2 = len(f.name)
fig = ("{name}|{o2:>2}\n"
"{space2} \/\n"
"{space2} /\\\n").format(name=f.name,
o2=f.right_overlap_size,
space2=" " * space2)
space = len(f.name)
for f in self.source_fragments[1:-1]:
name = "{o1:>2}|{name}|".format(o1=f.left_overlap_size,
name=f.name)
space2 = len(name)
fig += ("{space} {name}{o2:>2}\n"
"{space} {space2}\/\n"
"{space} {space2}/\\\n").format(
name=name,
o2=f.right_overlap_size,
space=" " * space,
space2=" " * space2)
space += space2
f = self.source_fragments[-1]
fig += ("{space} {o1:>2}|{name}").format(name=f.name,
o1=f.left_overlap_size,
space=" " * (space))
else:
'''
-|2577|61
| \/
| /\
| 61|5681|98
| \/
| /\
| 98|2389|557
| \/
| /\
| 557-
| |
--------------------------
'''
f = self.source_fragments[0]
space = len(f.name) + 3
fig = (" -|{name}|{o2:>2}\n"
"|{space}\/\n"
"|{space}/\\\n").format(name=f.name,
o2=f.right_overlap_size,
space=" " * space)
for f in self.source_fragments[1:]:
name = "{o1:>2}|{name}|".format(o1=f.left_overlap_size,
name=f.name)
space2 = len(name)
fig += ("|{space}{name}{o2:>2}\n"
"|{space}{space2}\/\n"
"|{space}{space2}/\\\n").format(
o2=f.right_overlap_size,
name=name,
space=" " * space,
space2=" " * space2)
space += space2
fig += "|{space}{o1:>2}-\n".format(
space=" " * (space),
o1=self.source_fragments[0].left_overlap_size)
fig += "|{space} |\n".format(space=" " * (space))
fig += " {space}".format(space="-" * (space + 3))
return pretty_str(dedent(fig))
def dbd_program(self):
'''Returns a string containing a text representation of a proposed
PCR program using a polymerase with a DNA binding domain such as Pfu-Sso7d.
::
Pfu-Sso7d (rate 15s/kb)
Three-step| 30 cycles | |Breslauer1986,SantaLucia1998
98.0°C |98.0°C | |SaltC 50mM
__________|_____ 72.0°C |72.0°C|Primer1C 1µM
00min30s |10s \ 61.0°C ________|______|Primer2C 1µM
| \______/ 0min 0s|10min |
| 10s | |4-8°C
'''
PfuSso7d_extension_rate = 15 #seconds/kB PCR product
extension_time_PfuSso7d = PfuSso7d_extension_rate * len(self) / 1000 # seconds
# Ta calculation for enzymes with dsDNA binding domains like Pfu-Sso7d
# https://www.finnzymes.fi/tm_determination.html
length_of_f = len(self.forward_primer.footprint)
length_of_r = len(self.reverse_primer.footprint)
if (length_of_f>20 and length_of_r>20 and self.tmf_dbd>=69.0 and self.tmr_dbd>=69.0) or (self.tmf_dbd>=72.0 and self.tmr_dbd>=72.0):
f=textwrap.dedent( '''
Pfu-Sso7d (rate {rate}s/kb)
Two-step| 30 cycles | |{size}bp
98.0°C |98.0C | |Breslauer1986,SantaLucia1998
_____ __|_____ | |SaltC {saltc:2}mM
00min30s|10s \ 72.0°C|72.0°C|Primer1C {forward_primer_concentration:3}µM
| \_______|______|Primer2C {reverse_primer_concentration:3}µM
| {0:2}min{1:2}s|10min |4-8°C
'''.format(rate = PfuSso7d_extension_rate,
forward_primer_concentration = self.forward_primer_concentration,
reverse_primer_concentration = self.rc,
saltc = self.saltc,
*divmod(extension_time_PfuSso7d,60),
size = len(self.seq)))
else:
if (length_of_f>20 and length_of_r>20):
ta = min(self.tmf_dbd,self.tmr_dbd)+3
else:
ta = min(self.tmf_dbd,self.tmr_dbd)
f=textwrap.dedent( '''
Pfu-Sso7d (rate {rate}s/kb)
Three-step| 30 cycles | |Breslauer1986,SantaLucia1998
98.0°C |98.0°C | |SaltC {saltc:2}mM
__________|_____ 72.0°C |72.0°C|Primer1C {forward_primer_concentration:3}µM
00min30s |10s \ {ta}°C ________|______|Primer2C {reverse_primer_concentration:3}µM
| \______/{0:2}min{1:2}s|10min |
| 10s | |4-8°C
'''.format(rate = PfuSso7d_extension_rate,
ta = math.ceil(ta),
forward_primer_concentration = self.forward_primer_concentration/1000,
reverse_primer_concentration = self.reverse_primer_concentration/1000,
saltc= self.saltc,
*divmod(extension_time_PfuSso7d,60)))
return pretty_str(f)
def figure(self):
'''
This method returns a simple figure of the two primers binding to a part
of the template.
::
5gctactacacacgtactgactg3
|||||||||||||||||||||| tm 52.6 (dbd) 58.3
5gctactacacacgtactgactg...caagatagagtcagtaaccaca3
3cgatgatgtgtgcatgactgac...gttctatctcagtcattggtgt5
|||||||||||||||||||||| tm 49.1 (dbd) 57.7
3gttctatctcagtcattggtgt5
Returns
-------
figure:string
A string containing a text representation of the primers
annealing on the template (see example above).
Notes
-----
tm in the figure above is the melting temperature (tm) for each primer calculated according to
SantaLucia 1998 [#]_.
dbd is the tm calculation for enzymes with dsDNA binding domains like Pfu-Sso7d [#]_. See [#]_
for more information.
References
----------
.. [#] J. SantaLucia, “A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-neighbor Thermodynamics,” Proceedings of the National Academy of Sciences 95, no. 4 (1998): 1460.
.. [#] M. Nørholm, “A Mutant Pfu DNA Polymerprimerase Designed for Advanced Uracil-excision DNA Engineering,” BMC Biotechnology 10, no. 1 (2010): 21, doi:10.1186/1472-6750-10-21.
.. [#] http://www.thermoscientificbio.com/webtools/tmc/
'''
f = '''
{sp1}5{faz}...{raz}3
{sp3}{rap} tm {tmr} (dbd) {tmr_dbd}
{sp3}3{rp}5
5{fp}3
{fap:>{fplength}} tm {tmf} (dbd) {tmf_dbd}
{sp2}3{fzc}...{rzc}5
'''.format( fp = self.forward_primer.seq,
fap = "|"*len(self.forward_primer.footprint),
fplength = len(self.forward_primer.seq),
tmf = round(self.tmf,1),
tmr = round(self.tmr,1),
tmf_dbd = round(self.tmf_dbd,1),
tmr_dbd = round(self.tmr_dbd,1),
rp = self.reverse_primer.seq[::-1],
rap = "|"*len(self.reverse_primer.footprint),
rplength = len(self.reverse_primer.seq),
faz = self.forward_primer.footprint,
raz = self.reverse_primer.footprint.reverse_complement(),
fzc = self.forward_primer.footprint.complement(),
rzc = self.reverse_primer.footprint[::-1],
sp1 = " "*(len(self.forward_primer.seq)-len(self.forward_primer.footprint)),
sp2 = " "*(len(self.forward_primer.seq)-len(self.forward_primer.footprint)),
sp3 = " "*(3+len(self.forward_primer.seq))
)
return pretty_str(textwrap.dedent(f).strip("\n"))
def url(self):
return pretty_str("http://www.ncbi.nlm.nih.gov/nucleotide/"+self.acc)
def url(self):
return pretty_str("http://www.ncbi.nlm.nih.gov/nucleotide/" + self.acc)
def test_reverse_complement(monkeypatch):
from pydna._pretty import pretty_str
from pydna.assembly import Assembly
from pydna.dseqrecord import Dseqrecord
a = Dseqrecord("acgatgctatactgtgCCNCCtgtgctgtgctcta")
#12345678901234
b = Dseqrecord("tgtgctgtgctctaTTTTTTTtattctggctgtatc")
#123456789012345
c = Dseqrecord("tattctggctgtatcGGGGGtacgatgctatactgtg")
a.name = "aaa" #1234567890123456
b.name = "bbb"
c.name = "ccc"
asm = Assembly((a, b, c), limit=14)
x = asm.assemble_circular()[0]
y = x.rc()
z = y.rc()
assert x.figure() == z.figure()
assert x.detailed_figure() == z.detailed_figure()
xfig = '''\
-|aaa|14
| \\/
| /\\
| 14|bbb|15
| \\/
| /\\
| 15|ccc|16
| \\/
| /\\
| 16-
| |
-----------------------
'''.rstrip()
xdfig = pretty_str('''\
||||||||||||||||
acgatgctatactgtgCCNCCtgtgctgtgctcta
TGTGCTGTGCTCTA
tgtgctgtgctctaTTTTTTTtattctggctgtatc
TATTCTGGCTGTATC
tattctggctgtatcGGGGGtacgatgctatactgtg
ACGATGCTATACTGTG
'''.rstrip() + "\n")
assert x.figure() == xfig
assert x.detailed_figure() == xdfig
yfig = '''\
-|ccc_rc|15
| \\/
| /\\
| 15|bbb_rc|14
| \\/
| /\\
| 14|aaa_rc|16
| \\/
| /\\
| 16-
| |
--------------------------------
'''.rstrip()
ydfig = '''\
||||||||||||||||
cacagtatagcatcgtaCCCCCgatacagccagaata
GATACAGCCAGAATA
gatacagccagaataAAAAAAAtagagcacagcaca
TAGAGCACAGCACA
tagagcacagcacaGGNGGcacagtatagcatcgt
CACAGTATAGCATCGT
'''.rstrip() + "\n"
assert y.figure() == yfig
assert y.detailed_figure() == ydfig