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)
del findsubstrings_suffix_arrays_python
except NameError:
pass
def delete_cache(delete=[ "amplify", "assembly", "genbank", "web", "synced" ]):
msg = ""
for file_ in delete:
msg += file_
try:
os.remove( os.path.join( os.environ["pydna_data_dir"], file_) )
msg += " deleted.\n"
except OSError, e:
if e.errno == errno.ENOENT:
msg += " no file to delete.\n"
return pretty_str(msg)
def open_cache():
if sys.platform=='win32':
subprocess.Popen(['start', os.environ["pydna_data_dir"]], shell= True)
elif sys.platform=='darwin':
subprocess.Popen(['open', os.environ["pydna_data_dir"]])
else:
try:
subprocess.Popen(['xdg-open', os.environ["pydna_data_dir"]])
except OSError:
return "no cache to open."
from ._version import get_versions
__version__ = get_versions()['version']
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 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 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 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))
del findsubstrings_suffix_arrays_python
except NameError:
pass
def delete_cache(delete=["amplify", "assembly", "genbank", "web", "synced"]):
msg = ""
for file_ in delete:
msg += file_
try:
os.remove(os.path.join(os.environ["pydna_data_dir"], file_))
msg += " deleted.\n"
except OSError, e:
if e.errno == errno.ENOENT:
msg += " no file to delete.\n"
return pretty_str(msg)
def open_cache():
if sys.platform == 'win32':
subprocess.Popen(['start', os.environ["pydna_data_dir"]], shell=True)
elif sys.platform == 'darwin':
subprocess.Popen(['open', os.environ["pydna_data_dir"]])
else:
try:
subprocess.Popen(['xdg-open', os.environ["pydna_data_dir"]])
except OSError:
return "no cache to open."
from ._version import get_versions
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))