def export_appendix(self):
appendix = []
appendix.append(Chapter('참조'))
content = Description()
endnotes = list(filter(lambda x: x.endnote != None, self.content))
for note in endnotes:
content.add_item(note.title, note.endnote)
appendix.append(content)
appendix = list(map(lambda x: x.dumps().replace('\\', '\\\\'), appendix))
return '\n'.join(appendix)
def test_lists():
# Lists
itemize = Itemize()
itemize.add_item(s="item")
itemize.append("append")
enum = Enumerate()
enum.add_item(s="item")
enum.append("append")
desc = Description()
desc.add_item(label="label", s="item")
desc.append("append")
def add_shopping_list(doc: Document, camp: Camp):
# content for this page
doc.append(Section('Einkaufsliste', numbering=False))
# space between colums
doc.append(Command('setlength'))
doc.append(Command('columnsep', arguments='40pt'))
doc.packages.add(Package('multicol'))
doc.packages.add(Package('enumitem'))
doc.packages.add(Package('setspace'))
for _ in range(1):
doc.append(Subsubsection('Gemüse und Früchte', numbering=False))
with doc.create(Multicols(arguments='2')) as multicols:
multicols.append(Command('small'))
with multicols.create(
Description(
options='leftmargin=1.75cm, itemsep=4pt')) as itemize:
# space between colums
itemize.append(
Command('setlength',
arguments=Command('itemsep'),
extra_arguments='0pt'))
itemize.append(
Command('setlength',
arguments=Command('parskip'),
extra_arguments='0pt'))
itemize.add_item('100g', 'the first item')
itemize.add_item('23 Stk.', 'Bananen')
itemize.add_item('100g', 'the first item')
itemize.add_item('10g', 'the item')
def generate_info_list(doc, testnumber):
section_name = 'Test {} results'.format(testnumber)
with doc.create(Section(section_name)):
with doc.create(Description()) as desc:
desc.add_item("\t", get_log(testnumber)[0])
desc.add_item("\t", get_log(testnumber)[1])
def test_lists():
# Lists
itemize = Itemize()
itemize.add_item(s="item")
itemize.append("append")
repr(itemize)
enum = Enumerate(enumeration_symbol=r"\alph*)", options={'start': 172})
enum.add_item(s="item")
enum.add_item(s="item2")
enum.append("append")
repr(enum)
desc = Description()
desc.add_item(label="label", s="item")
desc.append("append")
repr(desc)
def test_lists():
# Lists
itemize = Itemize()
itemize.add_item(s="item")
itemize.append("append")
repr(itemize)
empty_itemize = Itemize()
assert empty_itemize.dumps() == ''
repr(empty_itemize)
enum = Enumerate()
enum.add_item(s="item")
enum.append("append")
repr(enum)
desc = Description()
desc.add_item(label="label", s="item")
desc.append("append")
repr(desc)
def render(img_dir, img_name, pdf_name, output_list):
image_filename = os.path.join(img_dir, img_name)
geometry_options = {"tmargin": "1cm", "lmargin": "1cm"}
doc = Document(geometry_options=geometry_options)
with doc.create(Section("Xcos")):
with doc.create(Figure(position='h!')) as abs_pic:
abs_pic.add_image(image_filename, width='120px')
with doc.create(Description()) as desc:
for i in output_list:
for key, value in i.parameters().items():
desc.add_item(key, value)
doc.generate_pdf(pdf_name, clean_tex=False)
def generate_info_list(doc, testnumber):
"""
Generate a list which contains last 2 line of tests from log.txt
:param doc: LaTeX object, a instance of Document Class
:return: null
"""
section_name = 'Test' + str(testnumber) + ': Last 2 lines in log_test_' + str(testnumber ) + '.txt'
## Create a long table object in LaTeX object
with doc.create(Section(section_name)):
with doc.create(Description()) as desc:
desc.add_item("Second last line: ", get_log(testnumber)[0])
desc.add_item("Last line: ", get_log(testnumber)[1])
doc.append(NewPage())
def do():
doc = Document()
# create a bulleted "itemize" list like the below:
# \begin{itemize}
# \item The first item
# \item The second item
# \item The third etc \ldots
# \end{itemize}
with doc.create(Section('"Itemize" list')):
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"))
# create a numbered "enumerate" list like the below:
# \begin{enumerate}
# \item The first item
# \item The second item
# \item The third etc \ldots
# \end{enumerate}
with doc.create(Section('"Enumerate" list')):
with doc.create(Enumerate()) as enum:
enum.add_item("the first item")
enum.add_item("the second item")
enum.add_item(NoEscape("the third etc \\ldots"))
# create a labelled "description" list like the below:
# \begin{description}
# \item[First] The first item
# \item[Second] The second item
# \item[Third] The third etc \ldots
# \end{description}
with doc.create(Section('"Description" list')):
with doc.create(Description()) as desc:
desc.add_item("First", "The first item")
desc.add_item("Second", "The second item")
desc.add_item("Third", NoEscape("The third etc \\ldots"))
doc.generate_pdf('lists', clean_tex=False)
def test_lists():
# Lists
itemize = Itemize()
itemize.add_item(s="item")
itemize.append("append")
enum = Enumerate()
enum.add_item(s="item")
enum.append("append")
desc = Description()
desc.add_item(label="label", s="item")
desc.append("append")
def add_list(self, lists, type=1):
""" 添加列表
:param list lists: 列表名称
:param int type: 列表类型
:return: 无返回值
"""
if type == 1:
items = Itemize()
elif type == 2:
items = Enumerate()
elif type == 3:
items = Description()
else:
items = Itemize()
for item in lists:
items.add_item(item)
self.doc.append(items)
def add_meals(doc: Document, camp: Camp):
doc.packages.append(Package('xcolor'))
doc.packages.append(Package('tabularx'))
doc.packages.append(Package('colortbl'))
doc.packages.append(Package('enumitem'))
doc.packages.append(Package('float'))
doc.packages.append(Package('subcaption'))
doc.packages.append(
Package('caption',
options=[
NoEscape(r'textfont={large, bf}'), 'labelformat=empty',
'justification=raggedright'
]))
# for each meal
for meal in camp.get_meals_for_meal_page():
add_header(doc, meal)
# general Infos
with doc.create(Description()) as enum:
if meal['meal_gets_prepared']:
enum.add_item(
'Vorbereiten:',
'am ' + meal['meal_prepare_date'].strftime("%A %d. %b %Y"))
if meal['meal_description'] != '':
enum.add_item('Beschreibung / Notizen:',
meal['meal_description'])
# add recipes
if 'recipe' in meal:
for recipe in meal['recipe']:
add_recipe(doc, recipe)
else:
doc.append('Diese Mahlzeit enthält keine Rezepte.')
doc.append(Command(r'clearpage'))
doc.append(Command(r'pagebreak'))
def test_lists():
# Lists
itemize = Itemize()
itemize.add_item(s="item")
itemize.append("append")
repr(itemize)
enum = Enumerate(enumeration_symbol=r"\alph*)", options={'start': 172})
enum.add_item(s="item")
enum.add_item(s="item2")
enum.append("append")
repr(enum)
desc = Description()
desc.add_item(label="label", s="item")
desc.append("append")
repr(desc)
def add_message_to_doc(doc, message):
att_queryset = message.foiattachment_set.filter(
is_redacted=False,
is_converted=False
)
with doc.create(Description()) as descr:
descr.add_item(str(_('From:')), message.real_sender)
descr.add_item(str(_('To:')), message.get_text_recipient())
descr.add_item(str(_('Date:')),
formats.date_format(message.timestamp, "DATETIME_FORMAT"))
descr.add_item(str(_('Via:')), message.get_kind_display())
descr.add_item(str(_('URL:')), message.get_accessible_link())
descr.add_item(str(_('Subject:')), message.subject)
if len(att_queryset):
itemize = Itemize()
for att in att_queryset:
itemize.add_item(att.name)
descr.add_item(str(_('Attachments:')), itemize)
doc.append(NoEscape('\\noindent\\makebox[\\linewidth]{\\rule{\\textwidth}{1pt}}'))
doc.append(LineBreak())
append_text(doc, message.plaintext)
a = Axis(data=None, options=None)
p = Plot(name=None, func=None, coordinates=None, options=None)
# Utils
escape_latex(s='')
fix_filename(path='')
dumps_list(l=[], escape=False, token='\n')
bold(s='')
italic(s='')
verbatim(s='', delimiter='|')
# Lists
itemize = Itemize()
itemize.add_item(s="item")
itemize.append("append")
enum = Enumerate()
enum.add_item(s="item")
enum.append("append")
desc = Description()
desc.add_item(label="label", s="item")
desc.append("append")
def create_pdf(self):
# R1
# ----------------------------------------------------------------------------------
# 2) Put summary.txt and fastqc_data.txt files into dataframes then dictionaries
# i) Trimmed data
summary_df_trim = pd.read_table('%sR1_001.qfilter_fastqc/summary.txt' %
self.sample,
header=None,
names=['Score', 'Parameter'],
usecols=[0, 1])
score_list_trim = summary_df_trim['Score'].tolist(
) # not currently used, may be needed
parameter_list_trim = summary_df_trim['Parameter'].tolist()
sum_dict_trim = dict(zip(parameter_list_trim, score_list_trim))
# ii) Original non-trimmed data
summary_df = pd.read_table('%sR1_001_fastqc/summary.txt' % self.sample,
header=None,
names=['Score', 'Parameter'],
usecols=[0, 1])
score_list = summary_df_trim['Score'].tolist(
) # not currently used, may be needed
parameter_list = summary_df_trim['Parameter'].tolist()
sum_dict = dict(zip(parameter_list, score_list))
# basic stats files
# Trimmed data
basic_stats_df_trim = pd.read_table(
'%sR1_001.qfilter_fastqc/fastqc_data.txt' % self.sample,
header=None,
names=['Property', 'Value'],
usecols=[0, 1],
skiprows=3,
nrows=7)
property_list_trim = basic_stats_df_trim['Property'].tolist()
value_list_trim = basic_stats_df_trim['Value'].tolist()
stats_dict_trim = dict(zip(property_list_trim, value_list_trim))
# Original, non-trimmed data
basic_stats_df = pd.read_table('%sR1_001_fastqc/fastqc_data.txt' %
self.sample,
header=None,
names=['Property', 'Value'],
usecols=[0, 1],
skiprows=3,
nrows=7)
property_list = basic_stats_df['Property'].tolist()
value_list = basic_stats_df['Value'].tolist()
stats_dict = dict(zip(property_list, value_list))
# 3) Create PDF with basic statistics, summary data and png images
doc = Document()
doc.packages.append(
Package(
'geometry',
options=['tmargin=0.75in', 'lmargin=0.5in', 'rmargin=0.5in']))
doc.packages.append(Package('subcaption'))
doc.packages.append(Package('xcolor'))
doc.append(Command('makeatletter'))
doc.append(Command('setlength', NoEscape(r'\@fptop}{0pt')))
doc.append(Command('makeatother'))
doc.append(Command(NoEscape(r'renewcommand{\baselinestretch}'), '1.0'))
doc.append(Command('begin', 'center'))
doc.append(Command('Large', bold('Sample Quality Results')))
doc.append(Command('end', 'center'))
with doc.create(Section('Basic Statistics')):
with doc.create(Description()) as desc:
desc.add_item("Filename:", "%s" % stats_dict.get('Filename'))
desc.add_item("File type:", "%s" % stats_dict.get('File type'))
desc.add_item("Encoding:", "%s" % stats_dict.get('Encoding'))
with doc.create(Tabular(NoEscape(r'p{5.5cm}|c|c'))) as table:
table.add_row(('', 'Before trimming', 'After trimming'))
table.add_hline()
table.add_row(('Total Sequences',
'%s' % stats_dict.get('Total Sequences'),
'%s' % stats_dict_trim.get('Total Sequences')))
table.add_row(
('Sequences flagged as poor quality', '%s' %
stats_dict.get('Sequences flagged as poor quality'),
'%s' %
stats_dict_trim.get('Sequences flagged as poor quality')))
table.add_row(('Sequence length',
'%s' % stats_dict.get('Sequence length'),
'%s' % stats_dict_trim.get('Sequence length')))
table.add_row(('%GC', '%s' % stats_dict.get('%GC'),
'%s' % stats_dict_trim.get('%GC')))
with doc.create(Section('FastQC')):
with doc.create(
Figure(position='htbp',
placement=NoEscape(r'\centering'))):
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
plot.add_image('%s_fastqc/Images/per_base_quality.png' %
self.sample)
plot.add_caption(
'Per base sequence quality BEFORE trimming')
with doc.create(SubFigure()) as plot:
if sum_dict_trim.get(
'Per base sequence quality') == 'PASS':
colour = 'green'
elif sum_dict_trim.get(
'Per base sequence quality') == 'WARN':
colour = 'orange'
elif sum_dict_trim.get(
'Per base sequence quality') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%s.qfilter_fastqc/Images/per_base_quality.png' %
self.sample)
plot.add_caption(
NoEscape(
r'Per base sequence quality AFTER trimming \textcolor{%s}{%s}'
%
(colour,
sum_dict_trim.get('Per base sequence quality'))))
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '5 mm'))
plot.add_image(
'%s_fastqc/Images/per_sequence_gc_content.png' %
self.sample)
plot.add_caption('Per sequence GC content BEFORE trimming')
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '5 mm'))
if sum_dict_trim.get('Per sequence GC content') == 'PASS':
colour = 'green'
elif sum_dict_trim.get(
'Per sequence GC content') == 'WARN':
colour = 'orange'
elif sum_dict_trim.get(
'Per sequence GC content') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%s.qfilter_fastqc/Images/per_sequence_gc_content.png'
% self.sample)
plot.add_caption(
NoEscape(
r'Per sequence GC content AFTER trimming \textcolor{%s}{%s}'
% (colour,
sum_dict_trim.get('Per sequence GC content'))))
with doc.create(
Figure(position='htbp',
placement=NoEscape(r'\centering'))):
doc.append(Command('ContinuedFloat'))
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
plot.add_image(
'%s_fastqc/Images/sequence_length_distribution.png' %
self.sample)
plot.add_caption(
'Sequence Length Distribution BEFORE trimming')
with doc.create(SubFigure()) as plot:
doc.append(Command('hspace', '10 mm'))
if sum_dict_trim.get(
'Sequence Length Distribution') == 'PASS':
colour = 'green'
elif sum_dict_trim.get(
'Sequence Length Distribution') == 'WARN':
colour = 'orange'
elif sum_dict_trim.get(
'Sequence Length Distribution') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%s.qfilter_fastqc/Images/sequence_length_distribution.png'
% self.sample)
plot.add_caption(
NoEscape(
r'Sequence Length Distribution AFTER trimming \textcolor{%s}{%s}'
%
(colour,
sum_dict_trim.get('Sequence Length Distribution'))
))
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '10 mm'))
plot.add_image('%s_fastqc/Images/adapter_content.png' %
self.sample)
plot.add_caption('Adapter content BEFORE trimming')
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '10 mm'))
doc.append(Command('hspace', '10 mm'))
if sum_dict_trim.get('Adapter Content') == 'PASS':
colour = 'green'
elif sum_dict_trim.get('Adapter Content') == 'WARN':
colour = 'orange'
elif sum_dict_trim.get('Adapter Content') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%s.qfilter_fastqc/Images/adapter_content.png' %
self.sample)
plot.add_caption(
NoEscape(
r'Adapter content AFTER trimming \textcolor{%s}{%s}'
% (colour, sum_dict_trim.get('Adapter Content'))))
with doc.create(Section('BamStats')):
with doc.create(
Figure(position='htbp',
placement=NoEscape(r'\centering'))):
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
plot.add_image('%s.bwa.drm.sorted.bam.stats-quals-hm.png' %
self.sample)
plot.add_caption('Base quality per cycle')
with doc.create(SubFigure()) as plot:
doc.append(Command('hspace', '10 mm'))
plot.add_image(
'%s.bwa.drm.sorted.bam.stats-insert-size.png' %
self.sample)
plot.add_caption('Fragment size')
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '10 mm'))
plot.add_image('%s.bwa.drm.sorted.bam.stats-quals2.png' %
self.sample)
plot.add_caption('Quality per cycle')
pdflatex = '/usr/local/texlive/2015/bin/x86_64-linux/pdflatex'
doc.generate_pdf('%s_Sample_Quality' % self.sample,
clean_tex=False,
compiler=pdflatex)
a = Axis(data=None, options=None)
p = Plot(name=None, func=None, coordinates=None, options=None)
# Utils
escape_latex(s='')
fix_filename(path='')
dumps_list(l=[], escape=False, token='\n')
bold(s='')
italic(s='')
verbatim(s='', delimiter='|')
# Lists
itemize = Itemize()
itemize.add_item(s="item")
itemize.append("append")
enum = Enumerate()
enum.add_item(s="item")
enum.append("append")
desc = Description()
desc.add_item(label="label", s="item")
desc.append("append")
def create_pdf(self):
"""Creates the PDF using the PyLatex module.
Notes:-
"""
r1_summary_trim_dict, r1_stats_trim_dict, r2_summary_trim_dict = self.get_trimmed_data(
)
r1_stats_dict = self.get_original_data()
doc = Document()
doc.packages.append(Package('geometry', options=['margin=0.75in']))
doc.packages.append(Package('subcaption'))
doc.packages.append(Package('xcolor'))
doc.packages.append(Package('placeins'))
doc.append(Command('makeatletter'))
doc.append(Command('setlength', NoEscape(r'\@fptop}{0pt')))
doc.append(Command('makeatother'))
doc.append(Command(NoEscape(r'renewcommand{\baselinestretch}'), '1.0'))
doc.append(Command('begin', 'center'))
doc.append(Command('Large', bold('Sample Quality Results')))
doc.append(Command('end', 'center'))
with doc.create(Section('Basic Statistics')):
with doc.create(Description()) as desc:
desc.add_item("Sample:",
"%s" % r1_stats_dict.get('Filename')[:-16])
desc.add_item("File type:",
"%s" % r1_stats_dict.get('File type'))
desc.add_item("Encoding:",
"%s" % r1_stats_dict.get('Encoding'))
with doc.create(Tabular(NoEscape(r'p{5.5cm}|c|c'))) as table:
table.add_row(('', 'Before trimming', 'After trimming'))
table.add_hline()
table.add_row(
('Total Sequences',
'%s' % r1_stats_dict.get('Total Sequences'),
'%s' % r1_stats_trim_dict.get('Total Sequences')))
table.add_row((
'Sequences flagged as poor quality', '%s' %
r1_stats_dict.get('Sequences flagged as poor quality'),
'%s' %
r1_stats_trim_dict.get('Sequences flagged as poor quality')
))
table.add_row(
('Sequence length',
'%s' % r1_stats_dict.get('Sequence length'),
'%s' % r1_stats_trim_dict.get('Sequence length')))
table.add_row(('%GC', '%s' % r1_stats_dict.get('%GC'),
'%s' % r1_stats_trim_dict.get('%GC')))
with doc.create(Section('FastQC')):
with doc.create(
Figure(position='!htb',
placement=NoEscape(r'\centering'))) as fig:
fig.add_caption('Per base sequence quality')
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
plot.add_image(
'%sR1_001_fastqc/Images/per_base_quality.png' %
self.sample)
plot.add_caption('R1 BEFORE trimming')
with doc.create(SubFigure()) as plot:
if r1_summary_trim_dict.get(
'Per base sequence quality') == 'PASS':
colour = 'green'
elif r1_summary_trim_dict.get(
'Per base sequence quality') == 'WARN':
colour = 'orange'
elif r1_summary_trim_dict.get(
'Per base sequence quality') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR1_001.qfilter_fastqc/Images/per_base_quality.png' %
self.sample)
plot.add_caption(
NoEscape(r'R1 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r1_summary_trim_dict.get(
'Per base sequence quality'))))
with doc.create(SubFigure()) as plot:
plot.add_image(
'%sR2_001_fastqc/Images/per_base_quality.png' %
self.sample)
plot.add_caption('R2 BEFORE trimming')
with doc.create(SubFigure()) as plot:
if r2_summary_trim_dict.get(
'Per base sequence quality') == 'PASS':
colour = 'green'
elif r2_summary_trim_dict.get(
'Per base sequence quality') == 'WARN':
colour = 'orange'
elif r2_summary_trim_dict.get(
'Per base sequence quality') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR2_001.qfilter_fastqc/Images/per_base_quality.png' %
self.sample)
plot.add_caption(
NoEscape(r'R2 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r2_summary_trim_dict.get(
'Per base sequence quality'))))
with doc.create(
Figure(position='!htb',
placement=NoEscape(r'\centering'))) as fig:
fig.add_caption('Per sequence GC content')
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '5 mm'))
plot.add_image(
'%sR1_001_fastqc/Images/per_sequence_gc_content.png' %
self.sample)
plot.add_caption('R1 BEFORE trimming')
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '5 mm'))
if r1_summary_trim_dict.get(
'Per sequence GC content') == 'PASS':
colour = 'green'
elif r1_summary_trim_dict.get(
'Per sequence GC content') == 'WARN':
colour = 'orange'
elif r1_summary_trim_dict.get(
'Per sequence GC content') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR1_001.qfilter_fastqc/Images/per_sequence_gc_content.png'
% self.sample)
plot.add_caption(
NoEscape(r'R1 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r1_summary_trim_dict.get(
'Per sequence GC content'))))
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '5 mm'))
plot.add_image(
'%sR2_001_fastqc/Images/per_sequence_gc_content.png' %
self.sample)
plot.add_caption('R2 BEFORE trimming')
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '5 mm'))
if r2_summary_trim_dict.get(
'Per sequence GC content') == 'PASS':
colour = 'green'
elif r2_summary_trim_dict.get(
'Per sequence GC content') == 'WARN':
colour = 'orange'
elif r2_summary_trim_dict.get(
'Per sequence GC content') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR2_001.qfilter_fastqc/Images/per_sequence_gc_content.png'
% self.sample)
plot.add_caption(
NoEscape(r'R2 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r2_summary_trim_dict.get(
'Per sequence GC content'))))
with doc.create(
Figure(position='!htb',
placement=NoEscape(r'\centering'))) as fig:
fig.add_caption('Sequence Length Distribution')
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
plot.add_image(
'%sR1_001_fastqc/Images/sequence_length_distribution.png'
% self.sample)
plot.add_caption('R1 BEFORE trimming')
with doc.create(SubFigure()) as plot:
if r1_summary_trim_dict.get(
'Sequence Length Distribution') == 'PASS':
colour = 'green'
elif r1_summary_trim_dict.get(
'Sequence Length Distribution') == 'WARN':
colour = 'orange'
elif r1_summary_trim_dict.get(
'Sequence Length Distribution') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR1_001.qfilter_fastqc/Images/sequence_length_distribution.png'
% self.sample)
plot.add_caption(
NoEscape(r'R1 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r1_summary_trim_dict.get(
'Sequence Length Distribution'))))
with doc.create(SubFigure()) as plot:
plot.add_image(
'%sR2_001_fastqc/Images/sequence_length_distribution.png'
% self.sample)
plot.add_caption('R2 BEFORE trimming')
with doc.create(SubFigure()) as plot:
if r2_summary_trim_dict.get(
'Sequence Length Distribution') == 'PASS':
colour = 'green'
elif r2_summary_trim_dict.get(
'Sequence Length Distribution') == 'WARN':
colour = 'orange'
elif r2_summary_trim_dict.get(
'Sequence Length Distribution') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR2_001.qfilter_fastqc/Images/sequence_length_distribution.png'
% self.sample)
plot.add_caption(
NoEscape(r'R2 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r2_summary_trim_dict.get(
'Sequence Length Distribution'))))
with doc.create(
Figure(position='!htb',
placement=NoEscape(r'\centering'))) as fig:
fig.add_caption('Adapter Content')
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
plot.add_image(
'%sR1_001_fastqc/Images/adapter_content.png' %
self.sample)
plot.add_caption('R1 BEFORE trimming')
with doc.create(SubFigure()) as plot:
if r1_summary_trim_dict.get('Adapter Content') == 'PASS':
colour = 'green'
elif r1_summary_trim_dict.get('Adapter Content') == 'WARN':
colour = 'orange'
elif r1_summary_trim_dict.get('Adapter Content') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR1_001.qfilter_fastqc/Images/adapter_content.png' %
self.sample)
plot.add_caption(
NoEscape(
r'R1 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r1_summary_trim_dict.get('Adapter Content'))))
with doc.create(SubFigure()) as plot:
plot.add_image(
'%sR2_001_fastqc/Images/adapter_content.png' %
self.sample)
plot.add_caption('R2 BEFORE trimming')
with doc.create(SubFigure()) as plot:
if r2_summary_trim_dict.get('Adapter Content') == 'PASS':
colour = 'green'
elif r2_summary_trim_dict.get('Adapter Content') == 'WARN':
colour = 'orange'
elif r2_summary_trim_dict.get('Adapter Content') == 'FAIL':
colour = 'red'
else:
colour = 'black'
plot.add_image(
'%sR2_001.qfilter_fastqc/Images/adapter_content.png' %
self.sample)
plot.add_caption(
NoEscape(
r'R2 AFTER trimming \textcolor{%s}{%s}' %
(colour,
r2_summary_trim_dict.get('Adapter Content'))))
'''
doc.append(Command('FloatBarrier'))
with doc.create(Section('BamStats')):
with doc.create(Figure(position='htbp', placement=NoEscape(r'\centering'))):
doc.append(Command('centering'))
with doc.create(SubFigure()) as plot:
plot.add_image('%s.bwa.drm.sorted.bam.stats-quals-hm.png' % self.sample)
plot.add_caption('Base quality per cycle')
with doc.create(SubFigure()) as plot:
doc.append(Command('hspace', '10 mm'))
plot.add_image('%s.bwa.drm.sorted.bam.stats-insert-size.png' % self.sample)
plot.add_caption('Fragment size')
with doc.create(SubFigure()) as plot:
doc.append(Command('vspace', '10 mm'))
plot.add_image('%s.bwa.drm.sorted.bam.stats-quals2.png' % self.sample)
plot.add_caption('Quality per cycle')
'''
pdflatex = '/usr/local/texlive/2015/bin/x86_64-linux/pdflatex'
doc.generate_pdf('%s' % self.sample,
clean_tex=False,
compiler=pdflatex)
os.system(
'mv /home/cuser/PycharmProjects/amlpipeline/%s.pdf /media/sf_sarah_share/160620_M01622_0286_000000000-AR4UH/QC/'
% self.sample)
def export_endpaper(self):
options = ['itemsep=1pt', 'parsep=1pt']
book = Description(options=options)
book.add_item('제목', self.title)
book.add_item('저자', self.author)
book.add_item('편집', '미루')
book.add_item('디자인', '써드엔지니어링카르텔')
book.add_item('출간일', '2018-06-01')
publisher = Description(options=options)
publisher.add_item('출판', '금치산자레시피')
publisher.add_item('웹사이트', 'http://gtszrcp.com')
cover = Description(options=options)
cover.add_item('표지', NoEscape(self.cover.export_citation()))
cover.add_item('표지 그림 저작권', self.cover.license)
license = Description(options=options)
license.add_item('저작권', NoEscape('이 책에 수록된 저작물 중 별도로 표기되지 않은 모든 저작물의 저작권은 저자에게 있습니다. %s에 의해 이용할 수 있습니다.'%italic(self.license)))
license.add_item('', '이 책은 BartlebyMachine으로 제작되었습니다.')
endpaper = map(lambda x: x.dumps().replace('\\', '\\\\'), [
book, publisher, cover, license
])
return '\n'.join(list(endpaper))
# you can append to existing items
itemize.append(Command("ldots"))
# create a numbered "enumerate" list like the below:
# \begin{enumerate}
# \item The first item
# \item The second item
# \item The third etc \ldots
# \end{enumerate}
with doc.create(Section('"Enumerate" list')):
with doc.create(Enumerate()) as enum:
enum.add_item("the first item")
enum.add_item("the second item")
enum.add_item(NoEscape("the third etc \\ldots"))
# create a labelled "description" list like the below:
# \begin{description}
# \item[First] The first item
# \item[Second] The second item
# \item[Third] The third etc \ldots
# \end{description}
with doc.create(Section('"Description" list')):
with doc.create(Description()) as desc:
desc.add_item("First", "The first item")
desc.add_item("Second", "The second item")
desc.add_item("Third", NoEscape("The third etc \\ldots"))
doc.generate_pdf('lists')
def create_pdf_indi(self, test_spec_dict, test_description, path, name):
array_dimension = self.metrics_dict['con_matrix'].shape
row_dimensions = array_dimension[0]
array = self.metrics_dict['TpFpFnTn'][0]
code = self.metrics_dict['class_code'][0]
doc = Document("metrics")
with doc.create(Section('Test description')):
doc.append(test_description)
with doc.create(Description()) as desc:
for key, value in test_spec_dict.iteritems():
desc.add_item(key, value)
section = Section('Metrics overview')
test4 = Subsection('Confusion Matrix')
crop_array = np.array([
'Spring Barly(1)', 'Winter Barley(10)', 'Winter Wheat(11)',
'Winter Rape(22)', 'Maize(216)'
])
# Create TN, TP, FP, FN table
table4 = Tabular('cccccc')
table4.add_hline()
table4.add_row(('', 'Spring Barly', 'Winter Barley', 'Winter Wheat',
'Winter Rape', 'Maize'))
table4.add_hline()
for x in range(0, row_dimensions):
table4.add_row([
crop_array[x], self.metrics_dict['con_matrix'][x][0],
self.metrics_dict['con_matrix'][x][1],
self.metrics_dict['con_matrix'][x][2],
self.metrics_dict['con_matrix'][x][3],
self.metrics_dict['con_matrix'][x][4]
])
table4.add_hline()
test4.append(table4)
test1 = Subsection('Rate matrix')
# Create TN, TP, FP, FN table
table1 = Tabular('cccccc')
table1.add_hline()
table1.add_row(("Class", 'True-Positive', 'False-Positive',
'False-Negative', 'True-Negative', 'Accuracy'))
table1.add_hline()
for x in range(0, row_dimensions):
table1.add_row([
self.metrics_dict['class_code'][x],
self.metrics_dict['TpFpFnTn'][x][0],
self.metrics_dict['TpFpFnTn'][x][1],
self.metrics_dict['TpFpFnTn'][x][2],
self.metrics_dict['TpFpFnTn'][x][3],
self.metrics_dict['Acc_Indi'][x]
])
table1.add_hline()
test1.append(table1)
test3 = Subsection('Class metrics')
table3 = Tabular('ccccc')
table3.add_hline()
table3.add_row(("Class", 'True-Positive Rate (TPR)', 'Precision',
'True-Negative Rate (TNR)', 'F1-Score'))
table3.add_hline()
for x in range(0, row_dimensions):
table3.add_row([
self.metrics_dict['class_code'][x],
self.metrics_dict['recall_all'][x],
self.metrics_dict['precision_all'][x],
self.metrics_dict['TNR'][x],
self.metrics_dict['f1_score_all'][x]
])
table3.add_hline()
test3.append(table3)
test2 = Subsection('Other')
table2 = Tabular('cc')
table2.add_hline()
table2.add_row(("Class", "Value"))
table2.add_hline()
table2.add_row(
["F1 Micro (Globally)", self.metrics_dict['f1_score_micro']])
table2.add_row(
["F1 Macro (Each label)", self.metrics_dict['f1_score_macro']])
table2.add_row([
"F1 Weighted (Each label)", self.metrics_dict['f1_score_weighted']
])
table2.add_hline()
table2.add_row(
["Recall Micro (Globally)", self.metrics_dict['recall_micro']])
table2.add_row(
["Recall Macro (Each label)", self.metrics_dict['recall_macro']])
table2.add_row([
"Recall Weighted (Each label)",
self.metrics_dict['recall_weighted']
])
table2.add_hline()
table2.add_row([
"Precision Micro (Globally)", self.metrics_dict['precision_micro']
])
table2.add_row([
"Precision Macro (Each label)",
self.metrics_dict['precision_macro']
])
table2.add_row([
"Precision Weighted (Each label)",
self.metrics_dict['precision_weighted']
])
table2.add_hline()
table2.add_row(["Kappa", self.metrics_dict['kappa_all']])
table2.add_row(
["Kappa (Linear weighted)", self.metrics_dict['kappa_linear']])
table2.add_row([
"Kappa (Quadratic weighted)", self.metrics_dict['kappa_quadratic']
])
table2.add_hline()
table2.add_row([
"Accuracy (Correct classified)", self.metrics_dict['accuracy_all']
])
table2.add_row([
"Accuracy (Normalized)", self.metrics_dict['accuracy_normalized']
])
table2.add_hline()
table2.add_row(["Jaccard (Sum)", self.metrics_dict['jaccard_all']])
table2.add_row(
["Jaccard (Average)", self.metrics_dict['jaccard_normalized']])
table2.add_hline()
table2.add_row([
"Zero-one classification loss (Misclassifications)",
self.metrics_dict['zero_one_all']
])
table2.add_row([
"Zero-one classification loss (Fraction of misclassifications)",
self.metrics_dict['zero_one_normalize']
])
table2.add_hline()
table2.add_row(["Hamming loss", self.metrics_dict['hamming_loss']])
test2.append(table2)
section.append(test4)
section.append(test1)
section.append(test3)
section.append(test2)
doc.append(section)
try:
doc.generate_pdf(name + '_' + 'Metrics', compiler='pdflatex')
except Exception:
print ""
shutil.move(name + '_' + 'Metrics' + '.pdf', path)
try:
os.remove(name + '_' + 'Metrics' + '.tex')
except OSError:
pass
try:
os.remove(name + '_' + 'Metrics' + '.log')
except OSError:
pass
try:
os.remove(name + '_' + 'Metrics' + '.aux')
except OSError:
pass
return
