def _add_overview(self, doc: Document, title: str = 'Overview') -> None:
"""Add overview section to document.
:param doc:
:param title:
:return:
"""
with doc.create(Section(title)):
doc.append('Overview of kernel search results.')
doc.append("\n")
doc.append(VerticalSpace("10pt"))
doc.append(LineBreak())
best_kern_short = str(self.best_gp_model)
best_kern_long = self.best_gp_model.covariance.infix_full
with doc.create(MiniPage()):
doc.append(bold("Best Kernel:"))
doc.append("\n")
doc.append(VerticalSpace("1pt"))
doc.append(LineBreak())
doc.append(italic("Short Form:"))
doc.append("\n")
doc.append(best_kern_short)
doc.append("\n")
doc.append(VerticalSpace("2.5pt"))
doc.append(LineBreak())
doc.append(italic("Long Form:"))
doc.append("\n")
doc.append(best_kern_long)
def make_doc(self, foirequest):
doc = Document(
lmodern=True,
geometry_options={
"a4paper": True,
"margin": "1in",
},
)
# Change font
doc.packages.append(Package('fontspec,xunicode,array'))
doc.packages.append(Package('sectsty'))
doc.preamble.append(NoEscape("\\usepackage{helvet}"))
doc.preamble.append(
NoEscape("\\sectionfont{\\fontsize{12}{15}\\selectfont}"))
# Adjust description list
doc.packages.append(Package('enumitem'))
doc.preamble.append(
NoEscape(
"\\setlist[description]{labelindent=0cm,style=multiline,leftmargin=1.5cm}"
))
# Hyphenation
doc.append(NoEscape("\\lefthyphenmin=5"))
doc.append(NoEscape("\\sloppy"))
# doc.preamble.append(Command('title', foirequest.title))
# doc.preamble.append(Command('author', foirequest.get_absolute_domain_short_url()))
# doc.preamble.append(Command('date', NoEscape('\\today')))
# doc.append(NoEscape('\\maketitle'))
# Set up header and footer
header = PageStyle("header")
with header.create(Foot("L")):
header.append(italic(settings.SITE_NAME))
with header.create(Head("C")):
header.append(foirequest.title)
with header.create(Foot("R")):
header.append(
str(
_('Request #{request_no}').format(
request_no=foirequest.pk)))
with header.create(Foot("C")):
header.append(
italic(NoEscape(r'Seite \thepage\ von \pageref{LastPage}')))
doc.preamble.append(header)
doc.change_document_style("header")
for i, message in enumerate(foirequest.messages):
last = i == len(foirequest.messages) - 1
add_message_to_doc(doc, message)
if not last:
doc.append(NewPage())
return doc
def test_utils():
# Utils
escape_latex(s='')
fix_filename(path='')
dumps_list(l=[], escape=False, token='\n')
bold(s='')
italic(s='')
verbatim(s='', delimiter='|')
def writeReportFree(filename, questions, results):
doc = prepareDocFree()
for i in range(len(questions)):
figpie = plot_module.preparePie(results[i])
figbar = plot_module.prepareBar(results[i])
writeQuestion(doc, questions[i], results[i], figpie, figbar)
if settings.eliminate:
doc.append(italic(bold("Not: ")))
doc.append(italic("Değerlendirmeye hepsi '{}' olarak işaretlenmiş cevaplar katılmamıştır.".format(settings.eliminate_choice)))
status = createPdf(doc, filename, settings.debug)
return status
def test_utils():
# Utils
escape_latex(s="")
fix_filename(path="")
dumps_list(l=[], escape=False, token="\n")
bold(s="")
italic(s="")
verbatim(s="", delimiter="|")
def test_utils():
# Utils
escape_latex(s='')
fix_filename(path='')
dumps_list(l=[], escape=False, token='\n')
bold(s='')
italic(s='')
verbatim(s='', delimiter='|')
def make_doc(self, foirequest):
doc = Document(
lmodern=True,
geometry_options={
"a4paper": True,
"margin": "1in",
},
)
# Change font
doc.packages.append(Package('fontspec,xunicode,array'))
doc.packages.append(Package('sectsty'))
doc.preamble.append(NoEscape("\\usepackage{helvet}"))
doc.preamble.append(NoEscape("\\sectionfont{\\fontsize{12}{15}\\selectfont}"))
# Adjust description list
doc.packages.append(Package('enumitem'))
doc.preamble.append(NoEscape("\\setlist[description]{labelindent=0cm,style=multiline,leftmargin=1.5cm}"))
# Hyphenation
doc.append(NoEscape("\\lefthyphenmin=5"))
doc.append(NoEscape("\\sloppy"))
# doc.preamble.append(Command('title', foirequest.title))
# doc.preamble.append(Command('author', foirequest.get_absolute_domain_short_url()))
# doc.preamble.append(Command('date', NoEscape('\\today')))
# doc.append(NoEscape('\\maketitle'))
# Set up header and footer
header = PageStyle("header")
with header.create(Foot("L")):
header.append(italic(settings.SITE_NAME))
with header.create(Head("C")):
header.append(foirequest.title)
with header.create(Foot("R")):
header.append(str(
_('Request #{request_no}').format(request_no=foirequest.pk)))
with header.create(Foot("C")):
header.append(italic(NoEscape(r'Seite \thepage\ von \pageref{LastPage}')))
doc.preamble.append(header)
doc.change_document_style("header")
for i, message in enumerate(foirequest.messages):
last = i == len(foirequest.messages) - 1
add_message_to_doc(doc, message)
if not last:
doc.append(NewPage())
return doc
def add_to_book(self, book: Book):
with book.create(MdFramed()) as box:
box.append(bold(self.name))
box.append(NoEscape("\\hspace*{\\fill}"))
box.append(bold(self.__get_cost()))
box.append(" ¥€$\n")
box.append(NoEscape(r"\noindent\rule{\columnwidth}{1pt}"))
box.append(LineBreak())
box.append(NoEscape(self.desc))
box.append(LineBreak())
box.append(LineBreak())
with box.create(Tabularx("X|l|r")) as tab:
for effect, perma_effect, effector in itertools.zip_longest(self.effects, self.permanent_effects, self.effectors):
row = []
if effect is not None:
row.append(effect + ":" + get_effect_str(self.effects[effect]))
else:
row.append("")
if perma_effect is not None:
row.append(perma_effect + ":" + get_effect_str(self.permanent_effects[perma_effect]))
else:
row.append("")
if effector is not None:
row.append(italic(effector.name))
else:
row.append("")
tab.add_row(row)
def createParagraph(self, doc, line):
# Normal Line
if line.lineType == "normal":
doc.append(line.content)
# Line with formula
if line.lineType == "math":
with doc.create(Alignat(numbering=True, escape=False)) as math_eq:
math_eq.append(line.content)
# Example Lines
if line.lineType == "example":
if not line.title == "":
doc.append(bold(line.title+"\n"))
else:
doc.append(italic(line.content))
if line.lineType == "image":
imgPath = self.findImageAndConvert(
line.content)
if not imgPath == None:
with doc.create(Figure(position='H')) as image:
image.add_image(
imgPath)
return doc
def arxiv_search(search_query):
url = 'http://export.arxiv.org/api/query?search_query=all:' + \
search_query + '&start=0&max_results=5'
data = urllib.request.urlopen(url).read()
soup = bs(data, features='xml')
title_array = []
summary_array = []
for i in soup.findAll('title'):
title_array.append(i)
for i in soup.findAll('summary'):
summary_array.append(i)
doc = Document()
doc.packages.append(
Package(
'geometry',
options=[
'tmargin=1cm',
'lmargin=1cm',
'rmargin=1cm']))
with doc.create(Section('Search results for \"' + search_query + '\"')):
for i in range(1, 5):
doc.append(Subsection(italic(title_array[i].string)))
doc.append(summary_array[i].string)
doc.generate_pdf()
def append_liquor_list(doc, df, own_page):
# TODO no interaction with dataframe?
kinds = df[df.Category.isin(['Spirit', 'Vermouth',
'Liqueur'])][['Kind', 'Type']]
if own_page:
print "Appending list as new page"
doc.append(NewPage())
listing = SamepageEnvironment()
block = Center()
if not own_page:
block.append(HRuleFill())
block.append(Command('\\'))
block.append(VerticalSpace('16pt'))
block.append(TitleText("Included Ingredients"))
block.append(Command('\\'))
listing.append(block)
listing.append(VerticalSpace('12pt'))
cols = add_paracols_environment(listing, 2, '8pt', sloppy=False)
with cols.create(FlushRight()):
for item in kinds.Kind:
cols.append(LargeText(item))
cols.append(Command('\\'))
cols.append(Command('switchcolumn'))
with cols.create(FlushLeft()):
for item in kinds.Type:
cols.append(LargeText(italic(item)))
cols.append(Command('\\'))
doc.append(listing)
def latex(self):
_content = ""
for c in self.children:
_content += c.latex()
if self.delimiter == '/':
return italic(_content, escape=False)
elif self.delimiter == '*':
return bold(_content, escape=False)
def fill_document(self):
"""Add a section, a subsection and some text to the document."""
with self.create(Section('A section')):
self.append('Some regular text and some ')
self.append(italic('italic text. '))
with self.create(Subsection('A subsection')):
self.append('Also some crazy characters: $&#{}')
def question_with_help(phrase, vocabulary, doc):
dictionary = rnd_remove(phrase)
gapped_phrase = dictionary['phrase']
entry = phrase[dictionary['entry']]
doc.append(to_string(gapped_phrase))
doc.append('\n\n')
doc.append(italic(to_string(show_help(entry, phrase, vocabulary))))
def fill_document(self):
"""Add a section, a subsection and some text to the document."""
with self.create(Section('A section')):
self.append('Some regular text and some ')
self.append(italic('italic text. '))
with self.create(Subsection('A subsection')):
self.append('Also some crazy characters: $&#{}')
def addExperience(self, jobs):
self.doc.append(Command("begin", ["rSection", "Related Work Experience"]))
for job in jobs:
self.doc.append(Command("begin", ["rSubsection", job[0], italic(job[1]), job[2], '']))
self.doc.append(Command("item", job[3]))
self.doc.append(Command("end", "rSubsection"))
self.doc.append(Command("end", "rSection"))
def GENP(A, b):
section = Section('The first section')
n = len(A)
if b.size != n:
raise ValueError("Invalid argument: incompatible sizes between A & b.", b.size, n)
for pivot_row in range(n-1):
section.append("Considering Column " + (str)(pivot_row+1))
for row in range(pivot_row+1, n):
section.append(italic("Row" +(str)(row+1)))
section.append(Subsection('\t', data=[Math(data=["\tmultiplier", '=', A[row][pivot_row], " / ", A[pivot_row][pivot_row]])]))
multiplier = A[row][pivot_row]/A[pivot_row][pivot_row]
multiplier = round(multiplier,2)
section.append(Math(data=["\t\tmultiplier", '=', multiplier]))
section.append("\n")
#the only one in this column since the rest are zero
section.append("\tapplying multiplier to the row")
section.append(Math(data=[
NoEscape("\t\tr_"+(str)(row+1))," - ", multiplier,NoEscape("r_"+(str)(pivot_row+1))
]))
for col in range(pivot_row, n):
section.append(Math(data=["\t\t", A[row][col]," - (", multiplier, " x ", A[pivot_row][col], ")"]))
A[row][col] = A[row][col] - multiplier * A[pivot_row][col]
section.append(Math(data=["\t\t\t = ", A[row][col]]))
#Equation solution column
section.append(Math(data=["\t\t", b[row]," - (", multiplier, " x ", b[pivot_row], ")"]))
b[row] = b[row] - multiplier * b[pivot_row]
section.append(Subsection('\t\t\t', data=[Math(data=['=', b[row]])]))
section.append(Math(data=['A', '=', Matrix(A)]))
section.append(Math(data=['b', '=', b]))
section.append("\n")
section.append("Performing back substitution")
x = np.zeros(n)
k = n-1
section.append(Math(data=[NoEscape("\tr_"+(str)(k+1)),"=", b[k], " / ", A[k,k]]))
x[k] = round(b[k]/A[k,k],2)
section.append(Math(data=["\t\t= ", x[k]]))
k-=1
while k >= 0:
eqn = [NoEscape("\tr_"+(str)(k+1)),"=", b[k], " - "]
eqn.extend(print_dot(A[k,k+1:],x[k+1:]))
eqn.extend([" / ", A[k,k]])
section.append(Math(data=eqn))
x[k] = round((b[k] - np.dot(A[k,k+1:],x[k+1:]))/A[k,k],2)
section.append(Math(data=["\t\t= ", x[k]]))
k = k-1
return section
def render_metric(value, best, second, decimals, format_string):
if isinstance(value, numbers.Number):
rendered = format_string.format(value, prec=decimals)
if value == best:
rendered = bold(rendered)
elif value == second:
rendered = italic(rendered)
return rendered
else:
return value
def add_song_to_doc(doc, song):
"""Insert info for the given Song into the Document."""
doc.append(chapter(song.title))
doc.append(label(song.slug))
doc.append('By ')
doc.append(italic(song.author))
doc.append(NewLine())
doc.append(song.lyrics())
return doc
def fill_document(doc):
"""Add a section, a subsection and some text to the document.
:param doc: the document
:type doc: :class:`pylatex.document.Document` instance
"""
with doc.create(Section('A section')):
doc.append('Some regular text and some ')
doc.append(italic('italic text. '))
with doc.create(Subsection('A subsection')):
doc.append('Also some crazy characters: $&#{}')
def add_page2(self):
doc = self.m_doc
with doc.create(pl.Section('A section 2')):
doc.append('Some regular text and some ')
doc.append(italic('italic text. '))
with doc.create(pl.Figure(position='h!')) as kitten_pic:
kitten_pic.add_image("meso.png",
width=NoEscape(r'0.75\textwidth'))
doc.append(pl.NewPage())
def fill_document(doc):
with doc.create(Section('A section')):
doc.append('Some regular text and some ')
doc.append(italic('italic text. '))
doc.append(bold('bold text. '))
with doc.create(Subsection('A subsection')):
doc.append('Also some crazy characters: $&#{}')
doc.append(
NoEscape(
r"$$f'(a) = \lim_{x \to a} \frac{f(x) - f(a)}{x-a}$$"))
def complexStuff(doc):
with doc.create(Section('The simple stuff')):
doc.append('Some regular text and some')
doc.append(italic('italic text. '))
doc.append('\nAlso some crazy characters: $&#{}')
with doc.create(Subsection('Math that is incorrect')):
doc.append(Math(data=['2*3', '=', 9]))
with doc.create(Subsection('Table of something')):
with doc.create(Tabular('rc|cl')) as table:
table.add_hline()
table.add_row((1, 2, 3, 4))
table.add_hline(1, 2)
table.add_empty_row()
table.add_row((4, 5, 6, 7))
a = np.array([[100, 10, 20]]).T
M = np.matrix([[2, 3, 4], [0, 0, 1], [0, 0, 2]])
with doc.create(Section('The fancy stuff')):
with doc.create(Subsection('Correct matrix equations')):
doc.append(Math(data=[Matrix(M), Matrix(a), '=', Matrix(M * a)]))
with doc.create(Subsection('Alignat math environment')):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'\frac{a}{b} &= 0 \\')
agn.extend([Matrix(M), Matrix(a), '&=', Matrix(M * a)])
with doc.create(Subsection('Beautiful graphs')):
with doc.create(TikZ()):
plot_options = 'height=4cm, width=6cm, grid=major'
with doc.create(Axis(options=plot_options)) as plot:
plot.append(Plot(name='model', func='-x^5 - 242'))
coordinates = [
(-4.77778, 2027.60977),
(-3.55556, 347.84069),
(-2.33333, 22.58953),
(-1.11111, -493.50066),
(0.11111, 46.66082),
(1.33333, -205.56286),
(2.55556, -341.40638),
(3.77778, -1169.24780),
(5.00000, -3269.56775),
]
plot.append(Plot(name='estimate', coordinates=coordinates))
# with doc.create(Subsection('Cute kitten pictures')):
# with doc.create(Figure(position='h!')) as kitten_pic:
# kitten_pic.add_image(image_filename, width='120px')
# kitten_pic.add_caption('Look it\'s on its back')
doc.generate_pdf('full', clean_tex=False)
def fill_document(doc):
"""Adds a section, a subsection and some text to the document.
:param doc: the document
:type doc: :class:`pylatex.Document` instance
"""
with doc.create(Section('A section')):
doc.append('Some regular text and some ' + italic('italic text. '))
with doc.create(Subsection('A subsection')):
doc.append(escape_latex('Also some crazy characters: $&#{}'))
def format_recipe(recipe, display_opts):
""" Return the recipe in a paragraph in a samepage
"""
recipe_page = SamepageEnvironment()
name_line = LargeText(recipe.name)
if display_opts.origin and 'schubar original' in recipe.origin.lower():
name_line.append(superscript('*'))
#name_line.append(superscript(NoEscape('\dag')))
if display_opts.prices and recipe.max_cost:
price = util.calculate_price(recipe.max_cost, display_opts.markup)
name_line.append(DotFill())
name_line.append(superscript('$'))
name_line.append(price)
name_line.append('\n')
recipe_page.append(name_line)
if display_opts.prep_line:
recipe_page.append(
FootnoteText(recipe.prep_line(extended=True, caps=False) + '\n'))
if display_opts.info and recipe.info:
recipe_page.append(SmallText(italic(recipe.info + '\n')))
for item in recipe.ingredients:
recipe_page.append(item.str() + '\n')
if display_opts.variants:
for variant in recipe.variants:
recipe_page.append(HorizontalSpace('8pt'))
recipe_page.append(SmallText(italic(variant + '\n')))
if display_opts.examples and recipe.examples: # and recipe.name != 'The Cocktail':
for e in recipe.examples:
recipe_page.append(
FootnoteText(
"${cost:.2f} | {abv:.2f}% | {std_drinks:.2f} | {kinds}\n".
format(**e._asdict())))
recipe_page.append(Command('par'))
return recipe_page
def fill_document(doc):
"""Add a section, a subsection and some text to the document.
:param doc: the document
:type doc: :class:`pylatex.document.Document` instance
"""
with doc.create(Section('ِش سثؤفهخى')):
doc.append('إخع ساخعمي شمصشغس سحثشن فاث فقعفا')
doc.append(italic('فشمهؤ ؤخىفثىفس شقث شمسخ ىهؤث'))
with doc.create(Subsection('آثص ٍعلاسثؤفهخى')):
doc.append('بشةخعس ؤقشئغ ؤاشقشؤفثقس: $&#{}')
def fill_document(doc):
"""Add a section, a subsection and some text to the document.
:param doc: the document
:type doc: :class:`pylatex.document.Document` instance
"""
test = "je suis un titre plutot long mais court a lafois ciic"
with doc.create(Section(test)):
doc.append('Some regular text and some ')
doc.append(italic('italic text. '))
with doc.create(Subsection('A subsection')):
doc.append('Also some crazy characters: $&#{}')
def fill_document(doc):
"""Add a section, a subsection and some text to the document.
:param doc: the document
:type doc: :class:`pylatex.document.Document` instance
"""
with doc.create(Section("A section")):
doc.append("Some regular text and some ")
doc.append(italic("italic text. "))
with doc.create(Subsection("A subsection")):
doc.append("Also some crazy characters: $&#{}")
def render_table(self,
doc: Document,
name_override: Optional[LatexObject] = None,
toc_ref: Optional[str] = None,
extra_rows: Optional[List[Tuple[str, Any]]] = None) -> None:
"""Write this table into a LaTeX document.
Args:
doc: The LaTeX document to be appended to.
name_override: An optional replacement for this table's name field.
toc_ref: A reference to be added to the table of contents.
extra_rows: Any extra rows to be added to the table before the kwargs.
"""
with doc.create(Table(position='htp!')) as table:
table.append(NoEscape(r'\refstepcounter{table}'))
table.append(Label(Marker(name=str(self.fe_id), prefix="tbl")))
if toc_ref:
table.append(NoEscape(r'\addcontentsline{toc}{subsection}{' + escape_latex(toc_ref) + '}'))
with doc.create(Tabularx('|lX|', booktabs=True)) as tabular:
package = Package('xcolor', options='table')
if package not in tabular.packages:
# Need to invoke a table color before invoking TextColor (bug?)
tabular.packages.append(package)
package = Package('seqsplit')
if package not in tabular.packages:
tabular.packages.append(package)
tabular.add_row((name_override if name_override else bold(self.name),
MultiColumn(size=1, align='r|', data=TextColor('blue', self.fe_id))))
tabular.add_hline()
type_str = f"{self.type}"
match = re.fullmatch(r'^<.* \'(?P<typ>.*)\'>$', type_str)
type_str = match.group("typ") if match else type_str
tabular.add_row(("Type: ", escape_latex(type_str)))
if self.path:
if isinstance(self.path, LatexObject):
tabular.add_row(("", self.path))
else:
tabular.add_row(("", escape_latex(self.path)))
for k, v in self.fields.items():
tabular.add_hline()
tabular.add_row((f"{k.capitalize()}: ", v))
if self.args:
tabular.add_hline()
tabular.add_row(("Args: ", self.args))
if extra_rows:
for (key, val) in extra_rows:
tabular.add_hline()
tabular.add_row(key, val)
if self.kwargs:
tabular.add_hline()
for idx, (kwarg, val) in enumerate(self.kwargs.items()):
tabular.add_row((italic(kwarg), val), color='white' if idx % 2 else 'black!5')
def create_caption(section, superscript, text):
"""
Adds a caption preceded by superscripted characters to a table
:param section: LateX section object
:param superscript: character(s) to superscript
:param text: descriptive text
"""
section.append('\n')
# Superscript
section.append(bold(pl.NoEscape(r'{\footnotesize \textsuperscript {' + superscript + '}}')))
# Text
section.append(italic(pl.NoEscape(r'{\footnotesize {' + text + '}}')))
def create_reading_section(document, medium):
with document.create(Subsection('Reading')):
with document.create(Itemize()) as itemize:
try:
df = pd.read_csv(os.path.join(medium, 'reading.csv'))
except pd.errors.EmptyDataError:
return
for _, row in df.iterrows():
title = row.Title
link = row.Link
itemize.add_item(italic(title))
itemize.append(NewLine())
arguments = Arguments(link, link)
itemize.append(Command('href', arguments=arguments))
def fill_document(doc):
"""Add a section, a subsection and some text to the document.
:param doc: the document
:type doc: :class:`pylatex.document.Document` instance
"""
with doc.create(Section('Details of Original Notes')):
doc.append('Word count: ')
doc.append(italic('something'))
with doc.create(Subsection('Key Words')):
with doc.create(Itemize()) as itemize:
itemize.add_item("the first item")
itemize.add_item("the second item")
itemize.add_item("the third etc")
# you can append to existing items
itemize.append(Command("ldots"))
def add_text(doc):
(idoc, introfile) = add_section("introduction")
idoc.append('Some regular text and some ')
idoc.generate_tex(introfile)
(bdoc, backgroundfile) = add_section("background")
bdoc.append('Some regular text and some ' + italic('italic text. '))
bdoc.generate_tex(backgroundfile)
add_evaluation()
doc.append(Section('Introduction'))
doc.append(Command('input', arguments='introduction.tex'))
doc.append(Section('Background'))
doc.append(Command('input', arguments='background.tex'))
doc.append(Section('Experiments'))
doc.append(Command('input', arguments='evaluation.tex'))
return doc
def add_finding(doc, finding):
"""Add a section, a subsection and some text to the document.
:param doc: the document
:type doc: :class:`pylatex.document.Document` instance
"""
with doc.create(Subsection(finding.name)):
# doc.append(evidence.created_at)
doc.append(finding.description)
doc.append(italic('italic text. '))
for proof in finding.proofs:
project_path = os.path.join('projects', str(finding.project_id))
relative_path = os.path.join(
str(finding.id),
str(proof.id) + os.path.splitext(proof.path)[-1])
absolute_path = os.path.join(project_path, relative_path)
if os.path.exists(absolute_path):
add_proof(doc, proof, relative_path)
def _subtable(self, idx, subK, octets):
"""
Generates latex code for a ccsds keys table
Args:
* idx (int): the index of the current sub-table in case the
trousseau needs to be split into several tables
* subK (list of keys): the list of keys to generate table on
* octets (bool): corresponding to trousseau.octets
"""
titles = ('Name', 'Start', 'Len', 'Value')
table = Tabular('|'.join(['l'] + ['c'] * (len(titles) - 1)))
if idx > 0:
table.add_row((MultiColumn(len(titles),
align='c',
data=italic("Continued")), ))
table.add_row(titles)
unit = "octets" if octets else "bits"
table.add_hline()
table.add_hline()
start_bit = 0
for cle in subK:
if not cle.relative_only:
start_bit = cle.start
# if no padding, allows flexible len of the ccsdskey
the_len = cle.len if cle.pad else "[0..{:d}]".format(cle.len)
if cle.isdic:
if cle.dic_force is not None:
the_type = repr(cle.dic[cle.dic_force])
else:
the_type = repr(cle.dic.values())
else:
the_type = re.search(r'type *= *([\S ]+)',
getattr(cle._fctunpack, 'func_doc', ''))
if the_type is None:
the_type = '-'
else:
the_type = the_type.group(1)
table.add_row((cle.name, start_bit, the_len, the_type))
start_bit += cle.len
table.add_row((MultiColumn(len(titles), align='c',
data='"Start" and "Len" are given in {}'\
.format(unit)),))
return table
def render_metric(value, best, second, decimals, format_string,
highlight_top, relative_to):
if isinstance(value, numbers.Number):
if relative_to is None or relative_to == 0 or not np.isfinite(
relative_to):
# absolute number
rendered = format_string.format(value, prec=decimals)
else:
# percent
rendered = format_ratio_percent(value,
relative_to,
decimals=decimals)
if highlight_top:
if value == best:
rendered = bold(rendered)
elif value == second:
rendered = italic(rendered)
return rendered
else:
return value
def strip_tags(self, string):
while '\\' in string:
# Find slash, grab the text before the slash (left), find the other locations
# that are key - the braces - and grab the key and the emphaszied text, then
# send the rest of the rest of the string back through the while loop in case
# there are other tags that need to be stripped
# TODO: what happens if text is both italicized and underlined?
slashLocation = string.find('\\')
left = string[:slashLocation]
textStart = string.find('{')
tag = string[slashLocation + 1:textStart]
tagEnd = string.find('}')
emphasizedText = string[textStart + 1:tagEnd]
# if '\\' in emphasizedText:
# so ... with a double tag ... you have to
# update where the tagEnd is, put the left stuff in the document
# put the first tag in and the first part of the emphasized text in
# then the strip the tags from the new emphasized text
# and what do you do with the right side ... hmmmm
# self.strip_tags(emphasizedText)
# Append the text as appropriate
self.doc.append(left)
if tag == 'underline':
self.doc.append(Command('underline', emphasizedText))
elif tag == 'textit':
self.doc.append(italic(emphasizedText))
elif tag == 'textbf':
self.doc.append(bold(emphasizedText))
else:
self.doc.append(emphasizedText)
if string[tagEnd + 1:tagEnd + 2] == ' ': # Force a space
self.doc.append(bold(' '))
string = string[
tagEnd +
1:] # remove what was added to the doc already from the string
# After the while loop is done, if there is any string left, append it (it is not emphasized)
self.doc.append(string)
def createDocument(filename, documentResults):
doc = Document('full')
imageFilename = os.path.join(os.path.dirname(__file__), 'plots/Beni_Anliker.png')
with doc.create(Section('Leistungstest Feuerwehr Derendingen 2017', numbering=False)):
with doc.create(Subsection('Persönliche Daten', numbering=False)):
doc.append('Name ')
doc.append('\nAlter ')
doc.append('\nGrösse ')
doc.append(italic('\nitalic text. '))
with doc.create(Subsection('Aktuelle Testresultate', numbering=False)):
doc.append('Standweitsprung: ' + documentResults['slj'])
doc.append('\nGesamtpunktzahl Leistungstest: ' + documentResults['totalScore'] + ' von 125 Punkten = ' + documentResults['numberToLabel'])
with doc.create(Subsection('Längsschnittvergleich', numbering=False)):
with doc.create(Figure(position = 'h!')) as diagram:
diagram.add_image(imageFilename, width = '350px')
diagram.add_caption('Beurteilung: 1 = Ungenügend, 2 = Genügend, 3 = Gut, 4 = Sehr gut, 5 = Hervorragend')
#doc.generate_pdf(clean_tex=False)
#doc.generate_tex()
print(doc.dumps())
def setup_header_footer(doc, pdf_opts, display_opts):
# Header with title, tagline, page number right, date left
# Footer with key to denote someting about drinks
title = pdf_opts.title or '@Schubar'
if display_opts.prices:
tagline = 'Tips never required, always appreciated'
tagline = pdf_opts.tagline or 'Tips for your drinks never required, always appreciated'
else:
tagline = 'Get Fubar at Schubar on the good stuff'
tagline = pdf_opts.tagline or 'Get Fubar at Schubar, but, like, in a classy way'
hf = PageStyle("schubarheaderfooter",
header_thickness=0.4,
footer_thickness=0.4)
with hf.create(Head('L')):
hf.append(TitleText(title))
hf.append(Command('\\'))
hf.append(FootnoteText(italic(tagline)))
with hf.create(Head('R')):
hf.append(FootnoteText(time.strftime("%b %d, %Y")))
if display_opts.origin:
with hf.create(Foot('L')):
hf.append(superscript("*"))
#hf.append(superscript(NoEscape("\dag")))
hf.append(FootnoteText(r"Schubar Original"))
with hf.create(Foot('C')):
if display_opts.prices:
hf.append(HorizontalSpace('12pt'))
hf.append(
FootnoteText(
NoEscape(
r"\$ amount shown is recommended tip, calculated from cost of ingredients"
)))
with hf.create(Foot('R')):
hf.append(FootnoteText(Command('thepage')))
doc.preamble.append(hf)
doc.change_document_style("schubarheaderfooter")
v = VectorName(name='')
M = np.matrix([[2, 3, 4],
[0, 0, 1],
[0, 0, 2]])
m = Matrix(matrix=M, name='', mtype='p', alignment=None)
# Package
p = Package(name='', base='usepackage', options=None)
# PGFPlots
tikz = TikZ(data=None)
a = Axis(data=None, options=None)
p = Plot(name=None, func=None, coordinates=None, options=None)
# Utils
escape_latex(s='')
fix_filename(filename='')
dumps_list(l=[], escape=False, token='\n')
bold(s='')
italic(s='')
verbatim(s='', delimiter='|')
def GeneratePDF(pre1,pre2,pre,read1,read2,read,out,logger):
#Function to generate pdf report summary of all the stats
logger.info("Generating PDF report of summary data")
doc = Document()
doc.packages.append(Package('geometry', options=['tmargin=1cm','lmargin=1cm','rmargin=1cm']))
doc.preamble.append(Command('title', 'Combined Summary Report'))
doc.append(NoEscape(r'\maketitle'))
with doc.create(Section('Pre-Processing Data')):
doc.append(italic("This section contains the input read data before processing."))
with doc.create(Subsection('Base Quality Graph')):
doc.append(italic("This graph shows an overview of the range of quality values across all bases at each position in the FastQ file."))
if read == 'Na':
with doc.create(Figure(position='h!')) as pic:
pic.add_image("preFastqcMetrics/"+read1.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
pic.add_caption(pre1.split('/')[-1].split('.')[0])
with doc.create(Figure(position='h')) as pic2:
pic2.add_image("preFastqcMetrics/"+read2.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
pic2.add_caption(pre2.split('/')[-1].split('.')[0])
else:
with doc.create(Figure(position='h')) as pic2:
pic2.add_image("preFastqcMetrics/"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
pic2.add_caption(pre.split('/')[-1].split('.')[0])
with doc.create(Subsection('Per Base Sequence Content Graph')):
doc.append(italic("This graph plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called."))
if read == 'Na':
with doc.create(Figure(position='h!')) as pic:
pic.add_image("preFastqcMetrics/"+read1.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
pic.add_caption(pre1.split('/')[-1].split('.')[0])
with doc.create(Figure(position='h')) as pic2:
pic2.add_image("preFastqcMetrics/"+read2.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
pic2.add_caption(pre2.split('/')[-1].split('.')[0])
else:
with doc.create(Figure(position='h')) as pic2:
pic2.add_image("preFastqcMetrics/"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
pic2.add_caption(pre.split('/')[-1].split('.')[0])
with doc.create(Subsection('Data Summary')):
with doc.create(Itemize()) as itemize:
if read == 'Na':
itemize.add_item(pre1.split('/')[-1].split('.')[0])
with open(out+"/"+read1.split('/')[-1].split('.')[0]+"_preprocess_Summary.txt") as f:
for line in f:
doc.append(line)
itemize.add_item(pre2.split('/')[-1].split('.')[0])
with open(out+"/"+read2.split('/')[-1].split('.')[0]+"_preprocess_Summary.txt") as f:
for line in f:
doc.append(line)
else:
itemize.add_item(pre.split('/')[-1].split('.')[0])
with open(out+"/"+read.split('/')[-1].split('.')[0]+"_preprocess_Summary.txt") as f:
for line in f:
doc.append(line)
with doc.create(Section('Post-Processing Data')):
doc.append("")
with doc.create(Subsection('Base Quality Graph')):
doc.append(italic("This graph shows an overview of the range of quality values across all bases at each position in the FastQ file."))
if read == "Na":
with doc.create(Figure(position='h!')) as pic3:
pic3.add_image("postFastqcMetrics/"+read1.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
pic3.add_caption(pre1.split('/')[-1].split('.')[0])
with doc.create(Figure(position='h')) as pic4:
pic4.add_image("postFastqcMetrics/"+read2.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
pic4.add_caption(pre2.split('/')[-1].split('.')[0])
else:
with doc.create(Figure(position='h')) as pic4:
pic4.add_image("postFastqcMetrics/"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
pic4.add_caption(pre.split('/')[-1].split('.')[0])
with doc.create(Subsection('Per Base Sequence Content Graph')):
doc.append(italic("This graph plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called."))
if read == 'Na':
with doc.create(Figure(position='h!')) as pic:
pic.add_image("postFastqcMetrics/"+read1.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
pic.add_caption(pre1.split('/')[-1].split('.')[0])
with doc.create(Figure(position='h')) as pic2:
pic2.add_image("postFastqcMetrics/"+read2.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
pic2.add_caption(pre2.split('/')[-1].split('.')[0])
else:
with doc.create(Figure(position='h')) as pic2:
pic2.add_image("postFastqcMetrics/"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
pic2.add_caption(pre.split('/')[-1].split('.')[0])
with doc.create(Subsection('Data Summary')):
with doc.create(Itemize()) as itemize:
if read == 'Na':
itemize.add_item(pre1.split('/')[-1].split('.')[0])
with open(out+"/"+read1.split('/')[-1].split('.')[0]+"_postprocess_Summary.txt") as f:
for line in f:
doc.append(line)
itemize.add_item(pre2.split('/')[-1].split('.')[0])
with open(out+"/"+read2.split('/')[-1].split('.')[0]+"_postprocess_Summary.txt") as f:
for line in f:
doc.append(line)
else:
itemize.add_item(pre.split('/')[-1].split('.')[0])
with open(out+"/"+read.split('/')[-1].split('.')[0]+"_postprocess_Summary.txt") as f:
for line in f:
doc.append(line)
if os.path.exists(out+"/PostMappingMetrics.txt"):
with doc.create(Section('Post Mapping Data')):
doc.append("")
with doc.create(Subsection('Data Summary')):
with open(out+"/PostMappingMetrics.txt") as f:
for line in f:
doc.append(line)
if os.path.exists(out+"/"+out+".qual.heatmap.pdf"):
cmd = "sips -s format png "+out+"/"+out+".qual.heatmap.pdf --out "+out+"/"+out+".qual.heatmap.png"
os.system(cmd)
cmd = "sips -s format png "+out+"/"+out+".DupRate_plot.pdf --out "+out+"/"+out+".Duprate_plot.png"
os.system(cmd)
with doc.create(Subsection('Visual Summary')):
doc.append(italic("This graph shows an overview of the range of quality values across all bases at each position in the alignment file."))
with doc.create(Figure(position='h!')) as pic:
pic.add_image(out+".qual.heatmap.png", width='160px')
pic.add_caption("Alignment Quality")
doc.append(italic("This graph shows read duplication rate."))
with doc.create(Figure(position='h')) as pic2:
pic2.add_image(out+".DupRate_plot.png", width='160px')
pic2.add_caption("Duplication Rate")
with doc.create(Itemize()) as itemize:
itemize.add_item(italic("Sequence based: reads with identical sequence are regarded as duplicated reads."))
itemize.add_item(italic("Mapping based: reads mapped to the exactly same genomic location are regarded as duplicated reads."))
else:
logger.info("No Post Mapping Data available. The rest of the informtation can be accessed from 'Summary_Report.pdf'")
doc.generate_pdf(out+'/Summary_Report', clean=False)
def tabulateAll(self):
"""
Create a table that summarises all input variables and additive
components, including the constant kernel as baseline and the final
full additive model.
"""
# 1-D variables
ks = self.best1d[:]
# Baseline: constant kernel
ks.append(self.constker)
# Additive components, if not 1-D
for k in self.summands:
if len(k.getActiveDims()) > 1:
ks.append(k)
# Full additive model, if involves more than one additive term
best = self.history[-1]
if len(self.summands) > 1:
ks.append(best)
ks.sort(key=lambda k: round(k.getNLML(), 2))
ks.sort(key=lambda k: round(k.error(), 4))
data = ks[0].data
ds = data.getDataShape()
nlml_min = round(min([k.getNLML() for k in ks]), 2)
error_min = round(min([k.error() for k in ks]), 4)
doc = self.doc
with doc.create(pl.Table(position='htbp!')) as tab:
caption_str = "Classification performance of the full model, its additive components (if any), all input variables, and the baseline."
tab.add_caption(ut.NoEscape(caption_str))
t = pl.Tabular('rlrr')
# Header
t.add_hline()
t.add_row((
pl.MultiColumn(1, align='c', data='Dimensions'),
pl.MultiColumn(1, align='c', data='Kernel expression'),
pl.MultiColumn(1, align='c', data='NLML'),
pl.MultiColumn(1, align='c', data='Error') ))
t.add_hline()
# Entries
for k in ks:
if k is self.constker:
row = [
ut.italic('--', escape=False),
ut.italic('$' + k.latex() + '$ (Baseline)', escape=False),
ut.italic('{0:.2f}'.format(k.getNLML()), escape=False),
ut.italic(r'{0:.2f}\%'.format(k.error()*100), escape=False) ]
else:
dims = sorted(k.getActiveDims())
row = [
ut.NoEscape(', '.join([str(d + 1) for d in dims])),
ut.NoEscape('$' + k.latex() + '$'),
ut.NoEscape('{0:.2f}'.format(k.getNLML())),
ut.NoEscape(r'{0:.2f}\%'.format(k.error()*100)) ]
if round(k.getNLML(), 2) == nlml_min:
row[2] = ut.bold(row[2])
if round(k.error(), 4) == error_min:
row[3] = ut.bold(row[3])
t.add_row(tuple(row))
t.add_hline()
tab.append(ut.NoEscape(r'\centering'))
tab.append(t)
def tabulateVariables(self):
"""
Create a table that summarises all input variables.
"""
ks = self.best1d[:]
ks.append(self.constker)
ks.sort(key=lambda k: round(k.getNLML(), 2))
ks.sort(key=lambda k: round(k.error(), 4))
data = ks[0].data
ds = data.getDataShape()
nlml_min = round(min([k.getNLML() for k in ks]), 2)
error_min = round(min([k.error() for k in ks]), 4)
doc = self.doc
with doc.create(pl.Table(position='htbp!')) as tab:
tab.add_caption(ut.NoEscape("Input variables"))
t = pl.Tabular('rlrrrcrr')
# Header
t.add_hline()
t.add_row((
'',
'',
pl.MultiColumn(3, align='c', data='Statistics'),
pl.MultiColumn(3, align='c', data='Classifier Performance')
))
t.add_hline(start=3, end=8)
t.add_row((
pl.MultiColumn(1, align='c', data='Dimension'),
pl.MultiColumn(1, align='c', data='Variable'),
pl.MultiColumn(1, align='c', data='Min'),
pl.MultiColumn(1, align='c', data='Max'),
pl.MultiColumn(1, align='c', data='Mean'),
pl.MultiColumn(1, align='c', data='Kernel'),
pl.MultiColumn(1, align='c', data='NLML'),
pl.MultiColumn(1, align='c', data='Error') ))
t.add_hline()
# Entries
for k in ks:
if k is self.constker:
row = [
ut.italic('--', escape=False),
ut.italic('Baseline', escape=False),
ut.italic('--', escape=False),
ut.italic('--', escape=False),
ut.italic('--', escape=False),
ut.italic(k.shortInterp(), escape=False),
ut.italic('{0:.2f}'.format(k.getNLML()), escape=False),
ut.italic(r'{0:.2f}\%'.format(k.error()*100), escape=False) ]
else:
dim = k.getActiveDims()[0]
row = [
dim+1,
data.XLabel[dim],
'{0:.2f}'.format(ds['x_min'][dim]),
'{0:.2f}'.format(ds['x_max'][dim]),
'{0:.2f}'.format(ds['x_mu'][dim]),
k.shortInterp(),
ut.NoEscape('{0:.2f}'.format(k.getNLML())),
ut.NoEscape(r'{0:.2f}\%'.format(k.error()*100)) ]
if round(k.getNLML(), 2) == nlml_min:
row[6] = ut.bold(row[6])
if round(k.error(), 4) == error_min:
row[7] = ut.bold(row[7])
t.add_row(tuple(row))
t.add_hline()
tab.append(ut.NoEscape(r'\centering'))
tab.append(t)
from pylatex import Document, Section, Subsection, Tabular, Math, TikZ, Axis, \
Plot, Figure, Package
from pylatex.numpy import Matrix
from pylatex.utils import italic, escape_latex
import os
if __name__ == '__main__':
image_filename = os.path.join(os.path.dirname(__file__), 'kitten.jpg')
doc = Document()
doc.packages.append(Package('geometry', options=['tmargin=1cm',
'lmargin=10cm']))
with doc.create(Section('The simple stuff')):
doc.append('Some regular text and some ' + italic('italic text. '))
doc.append(escape_latex('\nAlso some crazy characters: $&#{}'))
with doc.create(Subsection('Math that is incorrect')):
doc.append(Math(data=['2*3', '=', 9]))
with doc.create(Subsection('Table of something')):
with doc.create(Tabular('rc|cl')) as table:
table.add_hline()
table.add_row((1, 2, 3, 4))
table.add_hline(1, 2)
table.add_empty_row()
table.add_row((4, 5, 6, 7))
a = np.array([[100, 10, 20]]).T
M = np.matrix([[2, 3, 4],
[0, 0, 1],
def main():
parser = argparse.ArgumentParser(prog='rnaseq',description="Program to help run RNA-seq Analysis")
required = parser.add_argument_group("Required Options")
required.add_argument('-t','--type',dest='type',help="Enter the type of analysis you want to do (F=Fast, S=Slow, N=Novel) [default=F]",choices=['F','S','N'],required=True, default="F")
required.add_argument('-f','--folder',dest='folder',help="Enter the location of the folder containing the reads", metavar="\b",default="Na",required=True)
required.add_argument('-i','--index',dest='index',help="Enter the location of the index file for the run u choose",default="Na",required=True)
parser.add_argument('-g','--gtf',dest='gtf',help="Enter the location of the gtf file", default='Na')
parser.add_argument('-m','--ribo',dest='ribo',help="Enter the location of the ribosomal file", default='Na')
args = parser.parse_args()
logger = logging.getLogger('Main')
logger.setLevel(logging.DEBUG)
stream = logging.StreamHandler()
stream.setLevel(logging.DEBUG)
formats = logging.Formatter('[%(asctime)s %(name)s %(levelname)s]: %(message)s')
stream.setFormatter(formats)
logger.addHandler(stream)
if not os.path.exists(args.index):
logger.error("The index file is not readable")
sys.exit()
reads = os.listdir(args.folder)
extension = ''
#Running the pipeline
for read in reads:
logger.info("Processing "+read+" ...")
out = read.split('/')[-1].split('.')[0]
read = args.folder+"/"+read
if args.type == "F" and not os.path.exists(out+"_Kallisto"):
call(["time","./rnaseq.py","-t","F","-r",read,"--kindex",args.index,"-l","54","-s","10","-o",out+"_Kallisto"])
logger.info("Ouputs written into "+out+"_Kallisto")
extension = "_Kallisto"
elif args.type == "S" and not os.path.exists(out+"_BWA"):
extra = ''
if args.ribo != 'Na':
extra = "-m "+args.ribo
call(["time","./rnaseq.py","-t","S","-r",read,"--bindex",args.index,"-o",out+"_BWA",extra])
logger.info("Ouputs written into "+out+"_BWA")
extension = "_BWA"
elif args.type == "N" and not os.path.exists(out+"_TopHat"):
extra = ''
if args.gtf != 'Na':
extra = "-g "+args.gtf
if args.ribo != 'Na':
extra = extra+" -m "+args.ribo
call(["time","./rnaseq.py","-t","N","-r",read,"--bowindex",args.index,"-o",out+"_TopHat",extra])
extension = "_TopHat"
else:
logger.info("Skipping this read as folder already exists...")
#Converging Report
doc = Document()
doc.packages.append(Package('geometry', options=['tmargin=1cm','lmargin=1cm','rmargin=1cm']))
with doc.create(Section('Base Quality Graph')):
doc.append(italic("This graph shows an overview of the range of quality values across all bases at each position in the FastQ file."))
extension = "_BWA"
for read in reads:
logger.info("Converging Pre Graphs Reports "+read+" ...")
out = read.split('/')[-1].split('.')[0]+extension
with doc.create(Figure(position='h!')) as baseQuality:
with doc.create(SubFigure(position='b',width=NoEscape(r'0.45\linewidth'))) as prepic:
prepic.add_image(out+"/preFastqcMetrics/triM"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
prepic.add_caption("Pre "+read.split('/')[-1].split('.')[0])
with doc.create(SubFigure(position='b',width=NoEscape(r'0.45\linewidth'))) as postpic:
postpic.add_image(out+"/postFastqcMetrics/triM"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_quality.png", width='160px')
postpic.add_caption("Post "+read.split('/')[-1].split('.')[0])
with doc.create(Section('Per Base Sequence Content Graph')):
doc.append(italic("This graph plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called."))
for read in reads:
out = read.split('/')[-1].split('.')[0]+extension
with doc.create(Figure(position='h!')) as baseQuality:
with doc.create(SubFigure(position='b',width=NoEscape(r'0.45\linewidth'))) as prepic:
prepic.add_image(out+"/preFastqcMetrics/triM"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
prepic.add_caption("Pre "+read.split('/')[-1].split('.')[0])
with doc.create(SubFigure(position='b',width=NoEscape(r'0.45\linewidth'))) as postpic:
postpic.add_image(out+"/postFastqcMetrics/triM"+read.split('/')[-1].split('.')[0]+"_fastqc/Images/per_base_sequence_content.png", width='160px')
postpic.add_caption("Post "+read.split('/')[-1].split('.')[0])
with doc.create(Section('Data Summary')):
doc.append(italic("This section contains post trimming FastQC summary results."))
for read in reads:
out = read.split('/')[-1].split('.')[0]+extension
with doc.create(Subsection(read)):
doc.append("")
with open(out+"/triM"+read.split('/')[-1].split('.')[0]+"_postprocess_Summary.txt") as f:
for line in f:
doc.append(line)
if os.path.exists(out+"/PostMappingMetrics.txt"):
with doc.create(Section('Post Mapping Data')):
doc.append("")
for read in reads:
out = read.split('/')[-1].split('.')[0]+extension
with doc.create(Subsection(read)):
with open(out+"/PostMappingMetrics.txt") as f:
for line in f:
doc.append(line)
if os.path.exists(out+"/"+out+".qual.heatmap.pdf"):
cmd = "sips -s format png "+out+"/"+out+".qual.heatmap.pdf --out "+out+"/"+out+".qual.heatmap.png"
os.system(cmd)
cmd = "sips -s format png "+out+"/"+out+".DupRate_plot.pdf --out "+out+"/"+out+".Duprate_plot.png"
os.system(cmd)
with doc.create(Section('Post Mapping Visual Data')):
doc.append("")
for read in reads:
out = read.split('/')[-1].split('.')[0]+extension
if os.path.exists(out+"/"+out+".qual.heatmap.png"):
with doc.create(Figure(position='h!')) as VisualSummary:
with doc.create(SubFigure(position='b',width=NoEscape(r'0.45\linewidth'))) as pic:
pic.add_image(out+"/"+out+".qual.heatmap.png", width='160px')
pic.add_caption("Alignment Quality")
with doc.create(SubFigure(position='b',width=NoEscape(r'0.45\linewidth'))) as pic2:
pic2.add_image(out+"/"+out+".DupRate_plot.png", width='160px')
pic2.add_caption("Duplication Rate")
VisualSummary.add_caption(read)
doc.generate_pdf('Summary_Report', clean=False)
#!/usr/bin/python3
import numpy as np
from pylatex import Document, Section, Subsection, Table, Math
from pylatex.numpy import Matrix
from pylatex.utils import italic
doc = Document()
section = Section('Yaay the first section, it can even be ' + italic('italic'))
section.append('Some regular text')
math = Subsection('Math', data=[Math(data=['2*3', '=', 6])])
section.append(math)
table = Table('rc|cl')
table.add_hline()
table.add_row((1, 2, 3, 4))
table.add_hline(1, 2)
table.add_empty_row()
table.add_row((4, 5, 6, 7))
table = Subsection('Table of something', data=[table])
section.append(table)
a = np.array([[100, 10, 20]]).T
M = np.matrix([[2, 3, 4],
[0, 0, 1],
[0, 0, 2]])
from pylatex import Document, Section, Subsection, Tabular, Math, TikZ, Axis, \
Plot, Figure, Package, Matrix
from pylatex.utils import italic
import os
if __name__ == '__main__':
image_filename = os.path.join(os.path.dirname(__file__), 'kitten.jpg')
doc = Document()
doc.packages.append(Package('geometry', options=['tmargin=1cm',
'lmargin=10cm']))
with doc.create(Section('The simple stuff')):
doc.append('Some regular text and some')
doc.append(italic('italic text. '))
doc.append('\nAlso some crazy characters: $&#{}')
with doc.create(Subsection('Math that is incorrect')):
doc.append(Math(data=['2*3', '=', 9]))
with doc.create(Subsection('Table of something')):
with doc.create(Tabular('rc|cl')) as table:
table.add_hline()
table.add_row((1, 2, 3, 4))
table.add_hline(1, 2)
table.add_empty_row()
table.add_row((4, 5, 6, 7))
a = np.array([[100, 10, 20]]).T
M = np.matrix([[2, 3, 4],
[0, 0, 1],
#!/usr/bin/python
import numpy as np
from pylatex import Document, Section, Subsection, Table, Math, TikZ, Axis, \
Plot
from pylatex.numpy import Matrix
from pylatex.utils import italic
doc = Document(filename='example_add')
section = doc.add(Section('Yaay the first section, it can even be ' + italic('italic')))
section.append('Some regular text')
section.add(Subsection('Math that is incorrect', data=[Math(data=['2*3', '=', 9])]))
table = Table('rc|cl')
table.add_hline()
table.add_row((1, 2, 3, 4))
table.add_hline(1, 2)
table.add_empty_row()
table.add_row((4, 5, 6, 7))
section.add(Subsection('Table of something', data=[table]))
a = np.array([[100, 10, 20]]).T
M = np.matrix([[2, 3, 4],
[0, 0, 1],
[0, 0, 2]])
math = Math(data=[Matrix(M), Matrix(a), '=', Matrix(M*a)])
section.add(Subsection('Matrix equation', data=[math]))
