def story(self):
story = list()
# iterate over qobjects
keeptogether_list = []
for qobject in self.obj.qobjects:
new, keeptogether = qobject.report.story()
new = list(new)
if len(new) == 0:
continue
if keeptogether:
keeptogether_list.extend(new)
else:
if len(keeptogether_list):
add = new.pop(0)
if isinstance(add, platypus.KeepTogether):
keeptogether_list.extend(add._content)
else:
keeptogether_list.append(add)
story.append(platypus.KeepTogether(keeptogether_list))
keeptogether_list = []
story.extend(new)
story.extend(keeptogether_list)
return story
def header(txt, style=HeaderStyleList[0], klass=platypus.Paragraph, sep=0.3):
"""Low-level interface func to ReportLab headers."""
s = platypus.Spacer(0.2 * inch, sep * inch)
para = klass(txt, style)
sect = [s, para]
result = platypus.KeepTogether(sect)
return result
def story(self):
story, tmp = Question.story(self)
if self.obj.calculate.range_count:
story.append(answers.Range(
self.obj.calculate.range_min,
self.obj.calculate.range_max,
self.obj.calculate.range_values,
self.obj.answers,
self.obj.calculate.mean,
self.obj.calculate.standard_deviation,
self.obj.calculate.count,
self.obj.calculate.significant))
if self.obj.calculate.count > 0 and self.obj.calculate.values:
for box in self.obj.boxes:
if box.value in self.obj.calculate.values:
story.append(
answers.Choice(
box.text,
self.obj.calculate.values[box.value],
False
)
)
story = [platypus.KeepTogether(story)]
return story, False
def story(self):
story, tmp = Question.story(self)
if len(self.text) > 0:
story.append(self.text[0])
story = [platypus.KeepTogether(story)]
if len(self.text) > 1:
story.extend(self.text[1:])
return story, False
def story(self):
story, tmp = Question.story(self)
if self.obj.calculate.count:
for i in range(len(self.obj.calculate.values)):
story.append(
answers.Choice(self.obj.answers[i],
self.obj.calculate.values[i],
self.obj.calculate.significant[i]))
story = [platypus.KeepTogether(story)]
return story, False
def story(self):
story, tmp = Question.story(self)
if self.obj.calculate.count:
story.append(
answers.Mark(self.obj.calculate.values.values(),
self.obj.answers, self.obj.calculate.mean,
self.obj.calculate.standard_deviation,
self.obj.calculate.count,
self.obj.calculate.significant))
story = [platypus.KeepTogether(story)]
return story, False
def story(self):
story, tmp = Question.story(self)
if self.obj.calculate.count:
for box in self.obj.boxes:
story.append(
answers.Choice(box.text,
self.obj.calculate.values[box.value],
self.obj.calculate.significant[box.value]))
story = [platypus.KeepTogether(story)]
if len(self.text) > 0:
story.append(platypus.Spacer(0, 3 * mm))
story.extend(self.text)
return story, False
def write_ingfoot(self):
# Ugly -- we know that heads comprise two elements -- a
# condbreak and a head...
ings = self.txt[2:]
if len(ings) > 4:
half = (len(ings) / 2)
first_half = ings[:-half]
second_half = ings[-half:]
t = platypus.Table([[first_half, second_half]])
t.hAlign = 'LEFT'
t.setStyle(
platypus.TableStyle([
('VALIGN', (0, 0), (1, 0), 'TOP'),
]))
self.txt = self.txt[:2] + [t]
self.txt = self.save_txt + [platypus.KeepTogether(self.txt)]
def getPreEl(self, txt):
s = platypus.Spacer(0.1 * inch, 0.1 * inch)
p = platypus.Preformatted(txt, PreStyle)
precomps = [s, p]
result = platypus.KeepTogether(precomps)
return result
def create_posts(url):
browser.get(url)
inp = input("Is the loading complete?")
src = browser.page_source
soup = BeautifulSoup(src, 'html.parser')
y = soup.findAll("mark")
cl1 = y[0].get("class")
cl2 = y[-1].get("class")
dont_look = ""
if cl1 != cl2:
dont_look = cl1
header = soup.select('h1')[0].text
header = '<link href="' + url + '">' + header + '</link>'
items = []
mainHeadline = platypus.Paragraph(header, mainHeadlineStyle)
items.append(mainHeadline)
posts.append(mainHeadline)
for m in y:
if (m.get("class") == dont_look):
continue
body = m.text
parent = m.parent
if parent.name == 'h1':
item = platypus.KeepTogether(items)
items = []
headline = platypus.Paragraph(parent.text, headlineStyle)
posts.append(headline)
items.append(headline)
else:
sib = parent.previous_sibling
t = False
if not sib:
t = True
else:
while sib.name != 'h1':
if not sib.previous_sibling:
sib = sib.parent
else:
sib = sib.previous_sibling
if not sib:
t = True
break
if (t):
para = platypus.Paragraph(body, paraStyle)
posts.append(para)
else:
if (sib.text == items[0].text):
para = platypus.Paragraph(body, paraStyle)
items.append(para)
posts.append(para)
else:
item = platypus.KeepTogether(items)
items = []
headline = platypus.Paragraph(sib.text, headlineStyle)
items.append(headline)
posts.append(headline)
para = platypus.Paragraph(body, paraStyle)
items.append(para)
posts.append(para)
def create_report(inbam1, invcf1, inbam2, invcf2, infasta, snpMatrix,
quantityWantSites, rows, output):
# Attempt to auto-detect sample names (experimental)
S1Name = (get_prefix(inbam1, invcf1)).rstrip('.fastq-reference')
S2Name = (get_prefix(inbam2, invcf2)).rstrip('.fastq-reference')
pairwiseSNPs = get_pairwiseSNPlist(snpMatrix, S1Name, S2Name)
pairwiseSNPpositions = pairwiseSNPs.keys()
if quantityWantSites > len(pairwiseSNPpositions):
print 'Selecting all {} putative SNP sites to print...'.format(len(pairwiseSNPpositions))
quantityWantSites = len(pairwiseSNPpositions)
randSitesUnsorted = random.sample(pairwiseSNPpositions, quantityWantSites) #randomly selected sites to investigate
randSitesUnsortedInts = [int(i) for i in randSitesUnsorted] #convert strings to integers
listWantSitesVCF = sorted(randSitesUnsortedInts, reverse=True) #for pileup report building
randSites = sorted(randSitesUnsortedInts)
vcfData1, vcfData2 = get_vcf_data(randSites, invcf1, invcf2)
if len(vcfData1) != len(vcfData2):
print 'ERROR: unequal number of SNPs identified between {} and {}'.format(S1Name, S2Name)
sys.exit('ERROR in VCF parsing')
numSites = len(vcfData1)
# Calculate page and frames
doc = Platypus.BaseDocTemplate(output, topMargin=0, bottomMargin=0, leftMargin=10, rightMargin=0)
doc.pagesize = landscape(A4) #ISO Code A4
# A4 Dimensions: 297 mm x 210 mm ; 11.69 in x 8.27 in ; 842 pt x 595 pt
frameCount = 2 #(numsites + (-numsites%6)) // 6
frameWidth = doc.height / frameCount
frameHeight = doc.width - .05 * inch
frames = []
# Construct a frame for each column
for frame in range(frameCount):
leftMargin = doc.leftMargin + frame * frameWidth
column = Platypus.Frame(leftMargin, doc.bottomMargin, frameWidth, frameHeight)
frames.append(column)
template = Platypus.PageTemplate(frames=frames)
doc.addPageTemplates(template)
PAGE_HEIGHT = defaultPageSize[0] #size in points
PAGE_WIDTH = defaultPageSize[1]
styles = getSampleStyleSheet()
style = styles['Normal']
style.fontName = 'Courier'
style.fontSize = 6.5
Title = ('Report containing {} of {} putative SNPs for {} and {}'.format(
str(quantityWantSites), str(len(pairwiseSNPpositions)),
os.path.basename(invcf1), os.path.basename(invcf2)))
report = [Paragraph(Title, styles['Heading2'])]
while numSites > 0:
# handle SNP sites at beginning of Chrom (<50 bases in)
posMinusFitty = (listWantSitesVCF[numSites - 1] - 50)
centeredPos = str(max(posMinusFitty, 0))
pos = str(vcfData1[numSites-1][0])
gap = Platypus.Spacer(0.25, 0.05*inch)
# vcfData lists are ordered: [pos, chrom, qual, DP, MQ, alt]
for sample in [[vcfData1, inbam1, S1Name], [vcfData2, inbam2, S2Name]]:
pileup = Platypus.Preformatted(get_ttview(sample[1], infasta,
(sample[0][1][1]), centeredPos, rows), style)
qual = sample[0][numSites-1][2]
DP = sample[0][numSites-1][3]
MQ = sample[0][numSites-1][4]
SNP = str(sample[0][numSites-1][5])
header = Paragraph('{} at position {} for {} with a QUAL of {}, MQ of {}, and raw read depth (DP) of {}'.format(
SNP, pos, sample[2], qual, MQ, DP), styles['Heading6'])
report.append(Platypus.KeepTogether([gap, header, pileup]))
numSites -= 1
doc.build(report)
def main():
args = parseArgs()
inbam = args.bam
infasta = args.fasta
invcf = args.vcf
numsites = args.numsites
output = args.output
rows = args.rows
SNPs, INDELs = get_vcf(invcf)
vcfSNPs = len(SNPs)
print 'Identified %s putative SNPs' % vcfSNPs
#print 'Identified %s putative INDEL bases' % len(INDELs)
# enable explicitly given positions (e.g., -p '89,3969181,44,123456') to investigate
if args.positions:
posList = [int(n) for n in args.positions.split(',')]
listWantSitesVCF = []
for i in posList:
if any(i in x for x in SNPs):
for SNP in SNPs:
if SNP[1] == i:
listWantSitesVCF.append(SNP)
else:
sys.exit('ERROR: specified position %s not a SNP' % i)
quantityWantSites = len(listWantSitesVCF)
listWantSitesVCF.reverse()
# randomly select SNP sites if positions (-p) unspecified
else:
quantityWantSites = int(numsites)
if quantityWantSites > vcfSNPs:
print 'Number of requested SNP sites to investigate exceeds number of identified SNPs'
print 'Selecting all %s putative SNP sites to print...' % vcfSNPs
quantityWantSites = vcfSNPs
randSitesUnsorted = random.sample(
SNPs, quantityWantSites) #randomly selected sites to investigate
listWantSitesVCF = sorted(randSitesUnsorted,
key=itemgetter(1),
reverse=True)
#calculate page and frames
doc = Platypus.BaseDocTemplate(output,
topMargin=0,
bottomMargin=0,
leftMargin=10,
rightMargin=0)
doc.pagesize = landscape(A4) #ISO Code A4
# A4 Dimensions: 297 mm x 210 mm ; 11.69 in x 8.27 in ; 842 pt x 595 pt
frameCount = 2 #(numsites + (-numsites%6)) // 6
frameWidth = doc.height / frameCount
frameHeight = doc.width - .05 * inch
frames = []
#construct a frame for each column
for frame in range(frameCount):
leftMargin = doc.leftMargin + frame * frameWidth
column = Platypus.Frame(leftMargin, doc.bottomMargin, frameWidth,
frameHeight)
frames.append(column)
template = Platypus.PageTemplate(frames=frames)
doc.addPageTemplates(template)
PAGE_HEIGHT = defaultPageSize[0] #size in points
PAGE_WIDTH = defaultPageSize[1]
styles = getSampleStyleSheet()
style = styles['Normal']
style.fontName = 'Courier'
style.fontSize = 6.5
Title = ('Report containing ' + str(quantityWantSites) + ' of ' +
str(vcfSNPs) + ' putative SNPs for ' + os.path.basename(invcf))
report = [Paragraph(Title, styles['Heading2'])]
while quantityWantSites > 0:
posMinusFitty = (listWantSitesVCF[quantityWantSites - 1][1] - 50)
centeredPos = max(
posMinusFitty,
0) #handles SNP sites at beginning of chrom (<50 bases in)
pileup = Platypus.Preformatted(
get_ttview(inbam, infasta,
listWantSitesVCF[quantityWantSites - 1][0], centeredPos,
rows), style)
pos = str(listWantSitesVCF[quantityWantSites - 1][1])
QUAL = str(listWantSitesVCF[quantityWantSites - 1][2])
DP = str(listWantSitesVCF[quantityWantSites - 1][3])
MQ = str(listWantSitesVCF[quantityWantSites - 1][4])
SNP = str(listWantSitesVCF[quantityWantSites - 1][5])
header = Paragraph(
SNP + ' at position ' + pos + ' with a QUAL of ' + QUAL +
', MQ of ' + MQ + ', and raw read depth (DP) of ' + DP,
styles['Heading6'])
gap = Platypus.Spacer(0.25, 0.05 * inch)
report.append(Platypus.KeepTogether([gap, header, pileup]))
quantityWantSites -= 1
doc.build(report)
def _create(self):
"""
Does the final creation of the Platypus Image object.
Including a correct numeration for the Figures list.
Typically this Method will be called by the _PreBuild-Method of
the Story class.
:return: story with all final objects for pdf rendering
:rtype: list of platypus objects ready for rendering.
"""
story = []
# Check if image is stored on disk
if isinstance(self._image, basestring) and (os.path.isfile(
self._image)):
# Create a Platypus Image from the given image path
img = utils.ImageReader(self._image)
imgw, imgh = img.getSize()
aspect = imgh / float(imgw)
lazy_value = 1
img_path = self._image
if self._mem_reduction is True:
# value 2 means "open the image when required then shut it"
lazy_value = 2
# the image is converted to JPEG only if it is a PNG
if what_image_type(self._image) is "png":
base_file_name_without_ext = os.path.splitext(
os.path.basename(self._image))[0]
full_dir_path = os.path.dirname(self._image)
img_path_jpeg = os.path.join(
full_dir_path,
base_file_name_without_ext + "." + "jpeg")
jpeg_image = pil_image.open(self._image)
jpeg_image.save(img_path_jpeg, "JPEG")
img_path = img_path_jpeg
img = plat.Image(img_path,
width=self._width,
height=(self._width * aspect),
lazy=lazy_value)
elif hasattr(self._image, 'wrapOn'):
img = self._image
else:
# unknown image or image with unsupported type
print(
"pdf build warning: unknown image type for image with caption: %s"
% self._name)
img = plat.Paragraph("unknown image type", NORMAL_STYLE)
self._halign = None
# align horizontally TO 'LEFT', 'CENTER' (default) or
# 'RIGHT' as supported by plat.Flowable
# use already set value if no change requested
if self._halign:
img.hAlign = self._halign
# Add Image
flowables = [plat.Spacer(1, 1 * cm), img]
# Add Title
if self._name is not None:
flowables.append(
plat.Paragraph(
"<b>%s %s</b>: %s" %
(self.FIGURE_CAPTION, self._build_figure_number_string(),
replace_html_chars(self._name)), self.STYLE))
flowables.append(plat.Spacer(1, 1 * cm))
# Add everything to story
story.append(plat.KeepTogether(flowables))
return story
