def pYPKa_ZE_ipynb_generator(tp, dir_="pYPKa_ZE_vectors"):
cwd = os.getcwd()
try:
os.makedirs(dir_)
except OSError as exception:
if exception.errno == errno.EEXIST:
pass
else:
print("The {} directory could not be created".format(dir_))
return None
os.chdir(dir_)
with open("standard_primers.txt","w") as f: f.write(read_data_file("standard_primers.txt"))
with open("pYPKa.gb","w") as f: f.write(read_data_file("pYPKa.gb"))
with open("pYPK_ZE.png","w") as f: f.write(read_bin_file("pYPK_ZE.png"))
with open(tp.id+".gb","w") as f: f.write(tp.format("gb"))
nbtemp = read_data_file("nb_template_pYPKa_ZE_insert.md")
name = "pYPKa_ZE_{}.ipynb".format(tp.id)
obj = notedown.MarkdownReader()
nb = obj.to_notebook(nbtemp.format(tp=tp.id))
pp = ExecutePreprocessor()
pp.timeout = 120 # seconds
pp.interrupt_on_timeout = True
shell = InteractiveShell.instance()
nb_executed, resources = pp.preprocess(nb, resources={})
g={}
l={}
from io import StringIO
old_stdout = sys.stdout
redirected_output = sys.stdout = StringIO()
for cell in nb.cells:
if cell.cell_type == 'code':
code = shell.input_transformer_manager.transform_cell(cell.source)
exec(code, g, l)
sys.stdout = old_stdout
nbformat.write(nb, name)
os.chdir(cwd)
return FileLinks(dir_)
gblink=gblink,
templatesize=templatesize,
insertseguid=insertseguid,
finalcseguidZ=finalcseguidZ,
finalcseguidE=finalcseguidE,
fpn=fp.name,
fps=fp.seq,
rpn=rp.name,
rps=rp.seq)
obj = notedown.MarkdownReader()
nb = obj.to_notebook(content)
pp = ExecutePreprocessor(timeout=600, kernel_name='python3')
pp.timeout = 120 # seconds
pp.interrupt_on_timeout = True
pp.preprocess(nb, resources={})
with open(newname, 'wt') as f:
nbformat.write(nb, f)
#os.chdir(cwd)
# with open("README_template.md", "r", encoding="utf8") as f:
# t=f.read()
# table = "| No. | TP | Promoter vector | Terminator vector | Jupyter nb |\n"
# table+= "|-----|----|-----------------|-------------------|------------|\n"
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
import os
import sys
from nbconvert.preprocessors.execute import ExecutePreprocessor
from nbconvert.nbconvertapp import NbConvertApp
from nbconvert.preprocessors import ExecutePreprocessor
from nbconvert.preprocessors.execute import CellExecutionError
import nbformat
folder = 'notebooks'
os.chdir(folder)
nb_list = [fname for fname in os.listdir('.') if fname.endswith('.ipynb')]
nb_list.sort()
ex = ExecutePreprocessor()
ex.timeout = 180 # seconds
ex.interrupt_on_timeout = True
has_error = False
for notebook in nb_list:
nb = nbformat.read(notebook, as_version=4)
try:
nb_executed, resources = ex.preprocess(nb, resources={})
except CellExecutionError as e:
print('Fail: %s \n%s\n\n' % (notebook, e.traceback[-1]))
has_error = True
os.chdir('..')
sys.exit(-1 if has_error else 0)
