def test_pydna_gbtext_clean():
from pydna.readers import read
from pydna.genbankfixer import gbtext_clean
files = [
("sequence.gb", "j2yAlBCZ-txSTCkakAmykAielRI"),
("NCBI_example.gb", "j2yAlBCZ-txSTCkakAmykAielRI"),
("YEplac181.txt", "lbnQtxi5LyDONRswRdG88-l8NF0"),
("pGADT7-Rec.gb", "rhnYE78wGKdqAZWiyVJzQ7HXXys"),
("P30350%20(2013-10-11%2013_49_14).dna.txt",
"_aEPoGLctHcOZdQdZIh-KyBt5WY"),
("ApE_example.gb", "c47i2ifiNZVvvnLQbX5anTVVoPE"),
("VectorNTI_example.gb", "bDPbx5P4yigGWh1zK7FiG_SF8qQ"),
("hej.txt", "lbnQtxi5LyDONRswRdG88-l8NF0"),
("fakeGenBankFile.gb", "ATrCXrjheFhltm8HhLJuFNtWXGw"),
]
for file_, seg in files:
with open("broken_genbank_files/" + file_, "r") as f:
infile = f.read()
if file_ == "hej.txt":
from Bio import BiopythonParserWarning
with pytest.warns(BiopythonParserWarning):
assert read(gbtext_clean(infile).gbtext).seguid() == seg
else:
assert read(gbtext_clean(infile).gbtext).seguid() == seg
def test_pydna_read_test():
from pydna.readers import read
print("sys.getdefaultencoding()", sys.getdefaultencoding())
import locale
print("locale.getpreferredencoding()", locale.getpreferredencoding())
assert read("pydna_read_test.txt").format(
"gb")[349:368] == '/label="2micron 2µ"'
def test_read_with_feature_spanning_ori():
from pydna.readers import read
test = '''
LOCUS New_DNA 10 bp ds-DNA circular 23-AUG-2018
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature join(9..10,1..2)
/locus_tag="myfeature"
/label="myfeature"
/ApEinfo_label="myfeature"
/ApEinfo_fwdcolor="cyan"
/ApEinfo_revcolor="green"
/ApEinfo_graphicformat="arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0"
ORIGIN
1 accgggtttt
//
'''
a = read(test)
assert str(a.seq).lower() == "accgggtttt"
assert str(a.features[0].extract(a).seq) == "TTAC"
assert a.features[0].strand == 1
b = a.rc()
assert str(b.seq).lower() == "aaaacccggt"
assert str(b.features[0].extract(a).seq) == "GTAA"
def test_ypk():
datafiles = '''pth1.txt|pYPK0_CiGXF1_PsXYL2.gb|iM8oDuvJPMPO995IdW3B0oo0Hkc
pth2.txt|pYPK0_SsXYL1_SsXYL2.gb|CB_qLhPgemW0XNLQOQEAdJKFujU
pth3.txt|pYPK0_NC_006038_CiGXF1_PsXYL2.gb|48_Bek9U1wxXlq1otmE7YHjYpnk
pth4.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1.gb|5OxynmwQA3br0cKAG8It7VVNGrg
pth5.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1_ScTAL1.gb|K8z4ijkYa0hA0KEOhv7-6PNJgBM
pth6.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1_ScTAL1.gb|K8z4ijkYa0hA0KEOhv7-6PNJgBM
pth7.txt|pYPK0_SsXYL1_SsXYL2_ScXKS1_ScTAL1.gb|K8z4ijkYa0hA0KEOhv7-6PNJgBM'''
for pYPKa_A in (True, False):
for datafile in textwrap.dedent(datafiles).split():
file_, name, code = datafile.split("|")
print()
print("############################")
print("datafile = ", file_)
print("pYPKa_A = ", pYPKa_A)
print("############################")
with open(file_, "r",) as f: text = f.read()
try:
shutil.rmtree(tmp)
except OSError:
pass
pw = pathway( parse(text), tmp, pYPKa_A=pYPKa_A)
s = read( os.path.join(tmp, name) )
with open(code+".txt") as f: c = f.read()
assert "".join( x for x in c.lower() if not x.isspace()) == str(s.seq).lower()
def test_cut_feat():
from pydna.readers import read
from pydna.amplify import pcr
from pydna.design import primer_design
from pydna.dseqrecord import Dseqrecord
from Bio.Restriction import EcoRI
puc19 = read('pUC19_MarkBudde.gb')
assert len(puc19.features) == 19
puc_lin = puc19[:]
assert len(puc_lin.features) == 19
ampl = primer_design(puc_lin)
pf, pr = ampl.forward_primer, ampl.reverse_primer
pcrProd = pcr(pf, pr, puc19)
assert len(pcrProd.features) == 21
assert len(pcrProd.cut(EcoRI)[1].features) == 16
def amplicon_to_dseqrecord(a):
d = Dseqrecord(a.seq)
d.features = a.features
return d
pcrProdDseqrecord = amplicon_to_dseqrecord(pcrProd)
assert len(pcrProdDseqrecord.cut(EcoRI)[1].features) == 16
def test_mark_budde():
""" test mark budde"""
a = read("pGREG505.gb")
assert a.name == "pGREG505"
assert a.looped().name == "pGREG505"
# assert a.annotations == "pGREG505"
assert a.id == "pGREG505"
assert a.looped().id == "pGREG505"
"""
def test_mark_budde():
''' test mark budde'''
a = read('pGREG505.gb')
assert a.name == "pGREG505"
assert a.looped().name == "pGREG505"
#assert a.annotations == "pGREG505"
assert a.id == "pGREG505"
assert a.looped().id == "pGREG505"
"""
def test_read_from_file():
from pydna.readers import read
from pydna.parsers import parse
a = read("read1.gb")
b = read("read2.gb")
c = read("read3.fasta")
d = read("read4.fasta")
x, y = parse("pth1.txt")
a.format("gb")
b.format("gb")
c.format("gb")
d.format("gb")
x.format("gb")
y.format("gb")
assert x.format()[3268:3278] == '2micron 2µ'
assert x.features[13].qualifiers['label'][0] == u'2micron 2µ'
assert str(a.seq).lower() == str(b.seq).lower() == str(
c.seq).lower() == str(d.seq).lower()
def test_read():
from pydna.readers import read
data = ""
with pytest.raises(ValueError):
read(data)
with pytest.raises(ValueError):
read(data, ds=False)
with pytest.raises(ValueError):
read(data, ds=True)
from pydna.readers import read
import os
import shutil
from pathlib import Path
cwd = os.getcwd()
outpath = Path.cwd() / "nb" # Path(cwd).parent.joinpath("pYPKa_ZE2")
outpath.mkdir(parents=True, exist_ok=True)
shutil.copy("pYPKa.gb", outpath)
shutil.copy("standard_primers.txt", outpath)
shutil.copy("figure_pYPKa_ZE.png", outpath)
pYPKa = read("pYPKa.gb")
with open("notebook_template_pYPKa_ZE.md", "r", encoding="utf8") as f:
t = f.read()
with open("tp_list.txt", "r") as f:
tps = [
l for l in f.read().splitlines() if l and not l.strip().startswith("#")
]
tp_dict = {}
lp = PrimerList()
for insertname, letter, pf, pr, comment in (x.split(maxsplit=4) for x in tps
if x):
from pydna.genbank import genbank
from pydna.design import primer_design
from pydna.amplify import pcr
from pydna.readers import read
from pydna.parsers import parse_primers
from pydna.assembly import Assembly
from pydna.gel import Gel
###############################################################################
saat = genbank("AF193791 REGION: 78..1895")
saat_pcr_prod = primer_design(saat)
pYPKa=read("pYPKa.gb")
from Bio.Restriction import AjiI
pYPKa_AjiI = pYPKa.linearize(AjiI)
pYPKa_A_saat = ( pYPKa_AjiI + saat_pcr_prod ).looped()
pYPKa_Z_prom = read("pYPKa_Z_TEF1.gb")
pYPKa_E_term = read("pYPKa_E_TPI1.gb")
p567,p577,p468,p467,p568,p578 = parse_primers('''
>567_pCAPsAjiIF (23-mer)
GTcggctgcaggtcactagtgag
>577_crp585-557 (29-mer)
def test_parse1():
from pydna.parsers import parse
from pydna.readers import read
''' test parsing fasta sequences from a text'''
text = '''
points....: 1
The sequence seq below represents a double stranded linear DNA molecule.
>seq
CTCCCCTATCACCAGGGTACCGATAGCCACGAATCT
Give the sequence(s) of the fragment(s) formed after digesting seq
with the restriction enzyme Acc65I in the order that they appear in seq.
Use FASTA format and give the Watson strand(s) in 5'-3' direction below.
Give the sequences the names frag1,frag2,... etc.
>frag1
CTCCCCTATCACCAGG
>frag2
GTACCGATAGCCACGAATCT
*********** Question 4 ***********
QuestionID:
'''
result = parse(text)
correct = [
'CTCCCCTATCACCAGGGTACCGATAGCCACGAATCT', 'CTCCCCTATCACCAGG',
'GTACCGATAGCCACGAATCT'
]
assert [str(s.seq) for s in result] == correct
assert [s.linear for s in result] == [True, True, True]
input = '''
LOCUS ScCYC1 330 bp DNA UNK 01-JAN-1980
DEFINITION ScCYC1
ACCESSION ScCYC1
VERSION ScCYC1
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 ATGACTGAAT TCAAGGCCGG TTCTGCTAAG AAAGGTGCTA CACTTTTCAA GACTAGATGT
61 CTACAATGCC ACACCGTGGA AAAGGGTGGC CCACATAAGG TTGGTCCAAA CTTGCATGGT
121 ATCTTTGGCA GACACTCTGG TCAAGCTGAA GGGTATTCGT ACACAGATGC CAATATCAAG
181 AAAAACGTGT TGTGGGACGA AAATAACATG TCAGAGTACT TGACTAACCC AAAGAAATAT
241 ATTCCTGGTA CCAAGATGGC CTTTGGTGGG TTGAAGAAGG AAAAAGACAG AAACGACTTA
301 ATTACCTACT TGAAAAAAGC CTGTGAGTAA
//
'''
result = parse(input).pop()
assert str(result.seq) == str(read(input).seq)
correct = '''ATGACTGAATTCAAGGCCGGTTCTGCTAAGAAAGGTGCTACACTTTTCAAGACTAGATGTCTACAATGCCACACCGTGGAAAAGGGTGGCCCACATAAGGTTGGTCCAAACTTGCATGGTATCTTTGGCAGACACTCTGGTCAAGCTGAAGGGTATTCGTACACAGATGCCAATATCAAGAAAAACGTGTTGTGGGACGAAAATAACATGTCAGAGTACTTGACTAACCCAAAGAAATATATTCCTGGTACCAAGATGGCCTTTGGTGGGTTGAAGAAGGAAAAAGACAGAAACGACTTAATTACCTACTTGAAAAAAGCCTGTGAGTAA'''
assert str(result.seq) == correct
assert result.linear == True
assert result.circular == False
seqs = parse('RefDataBjorn.fas')
assert len(seqs) == 771
assert list(set([len(a) for a in seqs])) == [901]
pAG25 = read("pAG25.gb")
assert pAG25.circular == True
assert pAG25.linear == False
pCAPs = read("pCAPs.gb")
assert pCAPs.circular == True
assert pCAPs.linear == False
pUC19 = read("pUC19.gb")
assert pUC19.circular == True
assert pUC19.linear == False
input = '''
ID example standard; DNA; UNC; 3 BP.
SQ Sequence 3 BP;
aaa 3
//
'''
result = parse(input).pop()
input = '''
ID name? standard; circular DNA; UNK; 100 BP.
XX
DT 25-DEC-2017
XX
DE description?.
XX
AC id?;
XX
SV id?
XX
KW .
XX
OS .
OC .
OC .
XX
FH Key Location/Qualifiers
SQ Sequence 100 BP;
aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 60
aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 100
//
'''
result = parse(input).pop()
def write(self, filename=None, f="gb"):
"""Writes the Dseqrecord to a file using the format f, which must
be a format supported by Biopython SeqIO for writing [#]_. Default
is "gb" which is short for Genbank. Note that Biopython SeqIO reads
more formats than it writes.
Filename is the path to the file where the sequece is to be
written. The filename is optional, if it is not given, the
description property (string) is used together with the format.
If obj is the Dseqrecord object, the default file name will be:
``<obj.locus>.<f>``
Where <f> is "gb" by default. If the filename already exists and
AND the sequence it contains is different, a new file name will be
used so that the old file is not lost:
``<obj.locus>_NEW.<f>``
References
----------
.. [#] http://biopython.org/wiki/SeqIO
"""
msg = ""
if not filename:
filename = "{name}.{type}".format(name=self.locus, type=f)
# generate a name if no name was given
if not isinstance(filename, str): # is filename a string???
raise ValueError("filename has to be a string, got",
type(filename))
name, ext = _os.path.splitext(filename)
msg = "<font face=monospace><a href='{filename}' target='_blank'>{filename}</a></font><br>".format(
filename=filename)
if not _os.path.isfile(filename):
with open(filename, "w") as fp:
fp.write(self.format(f))
else:
from pydna.readers import read
old_file = read(filename)
if self.seq != old_file.seq:
# If new sequence is different, the old file is renamed with "_OLD" suffix:
# TODO: add this timestamp so that all old versions are stored
# int(time.time() * 1000000) = 1512035297658778
old_filename = "{}_OLD{}".format(name, ext)
_os.rename(filename, old_filename)
msg = (
"<font color='DarkOrange ' face=monospace>"
"Sequence changed.<br>"
"</font>"
"<font color='red' face=monospace>"
"new: <a href='{filename}' target='_blank'>{filename}</a>     size: {nlen}bp topology: {ntop} SEGUID: {ns}<br>"
"</font>"
"<font color='green' face=monospace>"
"old: <a href='{oldfname}' target='_blank'>{oldfname}</a> size: {olen}bp topology: {otop} SEGUID: {os}<br>"
"</font>").format(
filename=filename,
oldfname=old_filename,
nlen=len(self),
olen=len(old_file),
ns=self.seguid(),
os=old_file.seguid(),
ntop={
True: "-",
False: "o"
}[self.linear],
otop={
True: "-",
False: "o"
}[old_file.linear],
)
with open(filename, "w") as fp:
fp.write(self.format(f))
elif "SEGUID" in old_file.description:
pattern = r"(lSEGUID|cSEGUID|SEGUID)_(\S{27})(_[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}\.[0-9]{6}){0,1}"
oldstamp = _re.search(pattern, old_file.description)
newstamp = _re.search(pattern, self.description)
newdescription = self.description
# print(oldstamp, newstamp)
if oldstamp and newstamp:
if oldstamp.group(0)[:35] == newstamp.group(0)[:35]:
newdescription = newdescription.replace(
newstamp.group(0), oldstamp.group(0))
elif oldstamp:
newdescription += " " + oldstamp.group(0)
newobj = _copy.copy(self)
newobj.description = newdescription
with open(filename, "w") as fp:
fp.write(newobj.format(f))
else:
with open(filename, "w") as fp:
fp.write(self.format(f))
return _display_html(_HTML(msg))
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from pydna.readers import read
from pathlib import Path
new = list(Path(".").glob("*.gb"))
old = list(Path("old").glob("*.gb"))
newset = set(n.name for n in new)
oldset = set(n.name for n in old)
for n in new:
ns = read(n)
op = Path("old") / Path(n)
if op.exists():
os = read(op)
print(n.name, ns.cseguid() == os.cseguid())
else:
print(n.name, "<<<<<<<<<<<<<<<<<<<<<<")
def pathway(pth, dir_="ypkassembly", pYPKa_A=True, print=print):
if len(pth)==0: # pth has to contain some sequences
print("No of sequences found.")
return None, None
names = [s.name for s in pth] # sequence names has to be unique
#if len(names)>len(set(names)):
# print("Gene names are not unique. Please rename sequences so that each sequence has a unique name.\n")
# print("Gene names parsed from Data page:\n\n")
# for name in names:
# print(name)
# return None, None
log=""
pYPK0 = read(read_data_file("pYPK0.gb"))
pYPKa = read(read_data_file("pYPKa.gb"))
from Bio.Restriction import ZraI, AjiI, EcoRV
files = {"standard_primers.txt" : read_data_file("standard_primers.txt"),
"pYPKa.gb" : read_data_file("pYPKa.gb"),
"pYPKpw.gb" : read_data_file("pYPKpw.gb"),
"tp_g_tp.png" : read_bin_file("tp_g_tp.png"),
"pYPK_ZE.png" : read_bin_file("pYPK_ZE.png"),
"pYPK_A.png" : read_bin_file("pYPK_A.png"),
"pw.png" : read_bin_file("pw.png"),
"start.bat" : read_data_file("start.bat"),
"start.sh" : read_data_file("start.sh"),}
cas_vectors = ""
tp_gene_tp_links = ""
pYPKa_clones=""
pwname = "pYPK0"
genes = 0
nbflag=False
while pth:
genes+=1
first = pth.pop(0)
# is sequence a tp-gene-tp vector?
if cloned(pYPK0, (ZraI, EcoRV), first):
m = re_cas.search(first.description)
if not m:
raise Exception( "{} is a pYPK0 tp-gene_tp sequence but was not correctly named.".format(last.description))
fn = first.description+".gb"
files[fn] = first.format("gb")
cas_vectors+= fn+"\n"
tp_gene_tp_links+= "\n[{}]({})\n".format( first.description, fn )
tp1_description = m.group(1)
gene_description = m.group(2)
tp2_description = m.group(3)
genes+=1
else:
try:
middle = pth.pop(0)
last = pth.pop(0)
except IndexError:
raise Exception("not enough sequences")
prom, gene, term = first, middle, last
if cloned(pYPKa, ZraI, prom):
m = re_Z.search(prom.description)
if not m:
raise Exception( "{} is a pYPKa_A_gene sequence but was incorrectly named.".format(gene.description))
prom_description = m.group(1)
files[m.group(0)+".gb"] = prom.format("gb")
else:
#print("Z"+str(files.has_key("pYPKa_ZE_{}.md".format(prom.id)))+prom.id)
if "pYPKa_ZE_{}.md".format(prom.id) not in files:
files[prom.id+".gb"] = prom.format("gb")
nbtemp = read_data_file("nb_template_pYPKa_ZE_insert.md")
files["pYPKa_ZE_{}.md".format(prom.id)] = nbtemp.format(tp=prom.id)
pYPKa_clones+="[pYPKa_ZE_{n}](pYPKa_ZE_{n}.ipynb) \n".format(n=prom.id)
prom_description = prom.id
if cloned(pYPKa, AjiI, gene):
m = re_A.search(gene.description)
if not m:
raise Exception( "{} is a pYPKa_A_gene sequence but was incorrectly named.".format(gene.description))
gene_description = m.group(1)
files[m.group(0)+".gb"] = gene.format("gb")
if not pYPKa_A:
nbflag=True
else:
n = "pYPKa_A_{}".format(gene.locus)
files[gene.locus+".gb"] = gene.format("gb")
if pYPKa_A:
nbtemp = read_data_file("nb_template_pYPKa_A_insert.md")
files[n+".md"] = nbtemp.format(insert=gene.locus)
gene_description = gene.locus
pYPKa_clones+="[{}]({}.ipynb) \n".format(n, n)
else:
gene_description = gene.locus
if cloned(pYPKa, EcoRV, term):
m = re_E.search(term.description)
if not m:
raise Exception( "{} is a pYPKa_A_gene sequence but was incorrectly named.".format(gene.description))
term_description = m.group(1)
files[m.group(0)+".gb"] = term.format("gb")
else:
#print("E"+str(files.has_key("pYPKa_ZE_{}.md".format(term.id)))+term.id)
if "pYPKa_ZE_{}.md".format(term.id) not in files:
files[term.id+".gb"] = term.format("gb")
nbtemp = read_data_file("nb_template_pYPKa_ZE_insert.md")
files["pYPKa_ZE_{}.md".format(term.id)] = nbtemp.format(tp=term.id)
pYPKa_clones+="[pYPKa_ZE_{n}](pYPKa_ZE_{n}.ipynb) \n".format(n=term.id)
term_description = term.id
x = "pYPK0_{}_{}_{}".format(prom_description, gene_description, term_description)
if pYPKa_A or nbflag:
nbtemp = read_data_file("nb_template_pYPK0_tp_gene_tp.md")
files[x+".md"] = nbtemp.format(tpz=prom_description,
gene=gene_description,
tpe=term_description)
else:
nbtemp = read_data_file("nb_template_pYPK0_tp_gene_tp_gap_repair.md")
files[x+".md"] = nbtemp.format(tpz=prom_description,
gene=gene.locus,
tpe=term_description)
nbflag=False
cas_vectors+="\n"+x+".gb\n"
tp_gene_tp_links+="[{}]({}.ipynb) \n".format(x, x)
pwname+="_{}".format(gene_description)
###########################################################################
obj = notedown.MarkdownReader()
cwd = os.getcwd()
try:
os.makedirs(dir_)
except OSError as exception:
if exception.errno == errno.EEXIST:
print("The {} directory already exists! Please delete or choose another name.".format(dir_))
else:
print("The {} directory could not be created".format(dir_))
return None, None
msg = "created subdirectory {}\n".format(dir_)
print(msg)
log+=msg
os.chdir(dir_)
msg = "\nsaving files sequence files and images..\n"
print(msg)
log+=msg
for name, content in sorted((n, c) for n, c in list(files.items()) if not n.endswith(".md")):
msg = "\nsaving: "+name
print(msg)
log+=msg
mode = {True:"wb", False:"w"}[hasattr(content, "decode")]
with open(name, mode) as f: #with open(name,"wb") as f:
f.write(content)
print("\n")
log+="\n"
msg = "\nsaving notebook files ..\n"
print(msg)
log+=msg
for name, content in sorted((n, c) for n, c in list(files.items()) if n.endswith(".md")):
newname = os.path.splitext(name)[0]+".ipynb"
msg = "\nsaving: "+newname
print(msg)
log+=msg
nb = nbformat.write(obj.to_notebook(content), newname)
pp = ExecutePreprocessor()
pp.timeout = 120 # seconds
pp.interrupt_on_timeout = True
print("\n")
log+="\n"
msg = "\nexecuting pYPKa notebooks..\n"
print(msg)
log+=msg
shell = InteractiveShell.instance()
#new_primers = []
g={}
l={}
pypkanbs = sorted([f for f in os.listdir(".") if re.match("pYPKa.+\.ipynb", f)])
if pypkanbs:
for name in pypkanbs:
msg = "\nexecuting: "+name
print(msg)
log+=msg
with io.open(name, 'r', encoding='utf-8') as f: nb = nbformat.read(f, 4)
nb_executed, resources = pp.preprocess(nb, resources={})
for cell in nb.cells:
if cell.cell_type == 'code':
code = shell.input_transformer_manager.transform_cell(cell.source)
exec(code, g, l)
#new_primers.extend( (l["fp"], l["rp"]) )
nbformat.write(nb, name)
g={}
l={}
else:
msg = "\nNo pYPKa notebooks found.\n"
print(msg)
log+=msg
print("\n")
log+="\n"
msg = "\nexecuting pYPK0 notebooks..\n"
print(msg)
log+=msg
g={}
l={}
resources={}
pypk0nbs = sorted([f for f in os.listdir(".") if re.match("pYPK0.+\.ipynb", f)])
if pypk0nbs:
for name in pypk0nbs:
msg = "\nexecuting: "+name
print(msg)
log+=msg
with io.open(name, 'r', encoding='utf-8') as f: nb = nbformat.read(f, 4)
nb_executed, resources = pp.preprocess(nb, resources={})
nbformat.write(nb, name)
for cell in nb.cells:
if cell.cell_type == 'code':
code = shell.input_transformer_manager.transform_cell(cell.source)
exec(code, g, l)
#try:
#new_primers.extend( (l["fp"], l["rp"]) )
#except KeyError:
# pass
g={}
l={}
else:
msg = "\nNo pYPK0 notebooks found.\n"
print(msg)
log+=msg
nbtemp = read_data_file("nb_template_pYPK0_pw.md")
#primer_list = "\n".join( p.format("tab") for p in new_primers )
#if new_primers:
# msg = u"\n\nsaving new_primers.txt..\n"
#with open("new_primers.txt","wb") as f: f.write("\n".join( p.format("fasta") for p in new_primers ))
#print("qwerty")
#print(pwname)
#print(os.path.basename(dir_))
#print(tp_gene_tp_links)
#print(add_space(cas_vectors, 17))
#print(pYPKa_clones)
#print(str(genes))
#print("123456789")
pwnb = nbtemp.format(name=pwname,
filename=os.path.basename(dir_),
tp_gene_tp_links = tp_gene_tp_links,
cas_vectors=add_space(cas_vectors, 17),
pYPKa_clones=pYPKa_clones,
length=genes)
nb = nbformat.write(obj.to_notebook(pwnb), "pw.ipynb")
#nb = nbformat.writes("pw.ipynb", obj.to_notebook(pwnb))
#with open("pw.ipynb", "w") as f: f.write(nb)
msg = "\n\nexecuting final pathway notebook..\n"
print(msg)
log+=msg
msg = "\nexecuting: pw.ipynb"
print(msg)
log+=msg
with io.open("pw.ipynb", 'r', encoding='utf-8') as f: nb = nbformat.read(f, 4)
nb_executed, resources = pp.preprocess(nb, resources={})
nbformat.write(nb, "pw.ipynb")
#for nb_ in [f for f in os.listdir(".") if f.endswith(".ipynb")]:
# subprocess.Popen(["ipython", "nbconvert", os.path.join(dir_, nb_)])
os.chdir(cwd)
fl = FileLink(os.path.join(dir_, "pw.ipynb"))
# pp = None
return fl, log
def test_longername_gives_deseq():
myseq = read(open("./broken_genbank_files/pGreenLantern1.gb", "r").read())
assert myseq.circular
myseq = read(open("./broken_genbank_files/fakeGenBankFile.gb", "r").read())
assert myseq.circular
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 10 08:03:27 2017
@author: bjorn
"""
from pydna.readers import read
template = read(">t\\ntacactcaccgtctatcattatctactatcgactgtatcatctgatagcac")
p1 = read(">p1\\ntacactcaccgtctatcattatc", ds=False)
p2 = read(">p2\\ngtgctatcagatgatacagtcg", ds=False)
# ann = pydna.Anneal((p1, p2), template)
def test_read_from_string():
from pydna.readers import read
input_ = '''
LOCUS New_DNA 4 bp ds-DNA linear 30-MAR-2013
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 2..3
/label=NewFeature
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 acgt
//
'''
a = read(input_)
assert str(a.seq) == "ACGT"
input_ = '''>hej
acgt'''
assert str(a.seq) == "ACGT"
input_ = '''
LOCUS New_DNA 4 bp ds-DNA linear 30-MAR-2013
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 2..3
/label=NewFeature
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 acgt
//
'''
a = read(input_)
assert str(a.seq) == "ACGT"
input_ = '''>hej
acgt'''
assert str(a.seq) == "ACGT"
input_ = '''>hej öööh!
acgt'''
assert str(a.seq) == "ACGT"
input_ = '''
LOCUS New_DNA 4 bp ds-DNA linear 30-MAR-2013
DEFINITION öööh!
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 2..3
/label=öööh!
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 acgt
//
'''
a = read(input_)
assert str(a.seq) == "ACGT"
