def _flowable(self, n):
tags = {
'name': lambda node: self.__name(node),
'para': lambda node: platypus.Paragraph(self._textual(node), self.styles.para_style_get(node), **(utils.attr_get(node, [], {'bulletText': 'str'}))),
'xpre': lambda node: platypus.XPreformatted(self._textual(node), self.styles.para_style_get(node), **(utils.attr_get(node, [], {'bulletText': 'str', 'dedent': 'int', 'frags': 'int'}))),
'pre': lambda node: platypus.Preformatted(self._textual(node), self.styles.para_style_get(node), **(utils.attr_get(node, [], {'bulletText': 'str', 'dedent': 'int'}))),
'illustration': lambda node: self._illustration(node),
'blockTable': lambda node: self._table(node),
'title': lambda node: platypus.Paragraph(self._textual(node), reportlab.lib.styles.getSampleStyleSheet()['Title'], **(utils.attr_get(node, [], {'bulletText': 'str'}))),
'h1': lambda node: platypus.Paragraph(self._textual(node), reportlab.lib.styles.getSampleStyleSheet()['Heading1'], **(utils.attr_get(node, [], {'bulletText': 'str'}))),
'h2': lambda node: platypus.Paragraph(self._textual(node), reportlab.lib.styles.getSampleStyleSheet()['Heading2'], **(utils.attr_get(node, [], {'bulletText': 'str'}))),
'h3': lambda node: platypus.Paragraph(self._textual(node), reportlab.lib.styles.getSampleStyleSheet()['Heading3'], **(utils.attr_get(node, [], {'bulletText': 'str'}))),
'image': lambda node: platypus.Image(node.getAttribute('file'), mask=(250, 255, 250, 255, 250, 255), **(utils.attr_get(node, ['width', 'height', 'preserveAspectRatio', 'anchor']))),
'spacer': lambda node: platypus.Spacer(
width=utils.unit_get(node.getAttribute('width') if node.hasAttribute('width') else '1cm'),
height=utils.unit_get(node.getAttribute('length'))),
'barCode': lambda node: code39.Extended39(self._textual(node)),
'pageBreak': lambda node: platypus.PageBreak(), # FIXME: it is not in RML std
'nextPage': lambda node: platypus.PageBreak(),
'condPageBreak': lambda node: platypus.CondPageBreak(**(utils.attr_get(node, ['height']))),
'setNextTemplate': lambda node: platypus.NextPageTemplate(str(node.getAttribute('name'))),
'nextFrame': lambda node: platypus.CondPageBreak(1000), # TODO: change the 1000 !
'ul': lambda node: self._list(node),
'keepInFrame': lambda node: self.__keep_in_frame(node),
}
retvalue = tags.get(n.localName)
if retvalue:
return retvalue(n)
else:
sys.stderr.write('Warning: flowable not yet implemented: %s !\n' % (n.localName,))
def _flowable(self, node):
if node.localName == 'para':
style = self.styles.para_style_get(node)
return platypus.Paragraph(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText': 'str'})))
elif node.localName == 'name':
self.styles.names[
node.getAttribute('id')] = node.getAttribute('value')
return None
elif node.localName == 'xpre':
style = self.styles.para_style_get(node)
return platypus.XPreformatted(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText': 'str', 'dedent': 'int', 'frags': 'int'})))
elif node.localName == 'pre':
style = self.styles.para_style_get(node)
return platypus.Preformatted(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText': 'str', 'dedent': 'int'})))
elif node.localName == 'illustration':
return self._illustration(node)
elif node.localName == 'blockTable':
return self._table(node)
elif node.localName == 'title':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Title']
return platypus.Paragraph(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText': 'str'})))
elif node.localName == 'h1':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading1']
return platypus.Paragraph(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText': 'str'})))
elif node.localName == 'h2':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading2']
return platypus.Paragraph(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText': 'str'})))
elif node.localName == 'h3':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading3']
return platypus.Paragraph(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText': 'str'})))
elif node.localName == 'image':
return platypus.Image(node.getAttribute('file'), mask=(250, 255, 250, 255, 250, 255), **(utils.attr_get(node, ['width', 'height', 'preserveAspectRatio', 'anchor'])))
elif node.localName == 'spacer':
if node.hasAttribute('width'):
width = utils.unit_get(node.getAttribute('width'))
else:
width = utils.unit_get('1cm')
length = utils.unit_get(node.getAttribute('length'))
return platypus.Spacer(width=width, height=length)
elif node.localName == 'barCode':
return code39.Extended39(self._textual(node))
elif node.localName == 'pageBreak':
return platypus.PageBreak()
elif node.localName == 'condPageBreak':
return platypus.CondPageBreak(**(utils.attr_get(node, ['height'])))
elif node.localName == 'setNextTemplate':
return platypus.NextPageTemplate(str(node.getAttribute('name')))
elif node.localName == 'nextFrame':
return platypus.CondPageBreak(1000) # TODO: change the 1000 !
elif node.localName == 'ul':
return self._list(node)
else:
sys.stderr.write(
'Warning: flowable not yet implemented: %s !\n' % (node.localName,))
return None
def elem2flow(self, elem, style, width):
"Convert this element to an iteration of flowables."
#print "elem2flow(%r)" % elem.__class__.__name__
if isinstance(elem, html.PRE):
assert len(elem.content) == 1
yield platypus.Preformatted(elem.content[0].text, style)
elif isinstance(elem, html.UL):
for li in elem.content:
istyle = self.getElementStyle(li, parent=elem)
for fl in self.elem2flow(li, istyle, width):
yield fl
elif isinstance(elem, html.LI):
yield self.makepar(elem.toxml(), style)
elif elem.__class__ is html.IMG:
yield platypus.Image()
elif isinstance(elem, html.TABLE):
t = self.pdftable(elem, width, style)
#pt=PdfTable(elem)
#t=pt.buildTable(width,style)
if t is None: return
#print "gonna yield", t
yield t
#elif elem.fragmentable:
elif isinstance(elem, html.Container):
#print "fragmentable %s" % elem.__class__.__name__
frags = []
for e in elem.content:
if e.fragmentable:
#print "gonna elem2frags(%s)"% e.__class__.__name__
for f in self.elem2frags(e, style):
frags.append(f)
elif e.flowable:
# found non-fragmentable element inside a flowable
if len(frags) > 0:
yield self.makepar("", style, frags=frags)
for ee in self.elem2flow(e, style, width):
yield ee
frags = []
## if e.__class__ is html.IMG:
## yield self.makepar("",style,frags=frags)
## yield platypus.Image()
## frags=[]
#elif e.__class__ is H1:
# yield self.makepar("",style,frags=frags)
yield self.makepar("", style, frags=frags)
#yield platypus.Table(data)
else:
raise "Cannot flow %r" % elem
def _flowable(self, node, extra_style=None):
if node.tag=='pto':
return self._pto(node)
if node.tag=='para':
style = self.styles.para_style_get(node)
if extra_style:
style.__dict__.update(extra_style)
result = []
for i in self._textual(node).split('\n'):
result.append(platypus.Paragraph(i, style, **(utils.attr_get(node, [], {'bulletText':'str'}))))
return result
elif node.tag=='barCode':
try:
from reportlab.graphics.barcode import code128
from reportlab.graphics.barcode import code39
from reportlab.graphics.barcode import code93
from reportlab.graphics.barcode import common
from reportlab.graphics.barcode import fourstate
from reportlab.graphics.barcode import usps
from reportlab.graphics.barcode import createBarcodeDrawing
except ImportError:
_logger.warning("Cannot use barcode renderers:", exc_info=True)
return None
args = utils.attr_get(node, [], {'ratio':'float','xdim':'unit','height':'unit','checksum':'int','quiet':'int','width':'unit','stop':'bool','bearers':'int','barWidth':'float','barHeight':'float'})
codes = {
'codabar': lambda x: common.Codabar(x, **args),
'code11': lambda x: common.Code11(x, **args),
'code128': lambda x: code128.Code128(str(x), **args),
'standard39': lambda x: code39.Standard39(str(x), **args),
'standard93': lambda x: code93.Standard93(str(x), **args),
'i2of5': lambda x: common.I2of5(x, **args),
'extended39': lambda x: code39.Extended39(str(x), **args),
'extended93': lambda x: code93.Extended93(str(x), **args),
'msi': lambda x: common.MSI(x, **args),
'fim': lambda x: usps.FIM(x, **args),
'postnet': lambda x: usps.POSTNET(x, **args),
'ean13': lambda x: createBarcodeDrawing('EAN13', value=str(x), **args),
'qrcode': lambda x: createBarcodeDrawing('QR', value=x, **args),
}
code = 'code128'
if node.get('code'):
code = node.get('code').lower()
return codes[code](self._textual(node))
elif node.tag=='name':
self.styles.names[ node.get('id')] = node.get('value')
return None
elif node.tag=='xpre':
style = self.styles.para_style_get(node)
return platypus.XPreformatted(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText':'str','dedent':'int','frags':'int'})))
elif node.tag=='pre':
style = self.styles.para_style_get(node)
return platypus.Preformatted(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText':'str','dedent':'int'})))
elif node.tag=='illustration':
return self._illustration(node)
elif node.tag=='blockTable':
return self._table(node)
elif node.tag=='title':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Title']
return platypus.Paragraph(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText':'str'})))
elif re.match('^h([1-9]+[0-9]*)$', (node.tag or '')):
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading'+str(node.tag[1:])]
return platypus.Paragraph(self._textual(node), style, **(utils.attr_get(node, [], {'bulletText':'str'})))
elif node.tag=='image':
image_data = False
if not node.get('file'):
if node.get('name'):
if node.get('name') in self.doc.images:
_logger.debug("Image %s read ", node.get('name'))
image_data = self.doc.images[node.get('name')].read()
else:
_logger.warning("Image %s not defined", node.get('name'))
return False
else:
import base64
newtext = node.text
if self.localcontext:
newtext = utils._process_text(self, node.text or '')
image_data = base64.decodestring(newtext)
if not image_data:
_logger.debug("No inline image data")
return False
image = StringIO(image_data)
else:
_logger.debug("Image get from file %s", node.get('file'))
image = _open_image(node.get('file'), path=self.doc.path)
return platypus.Image(image, mask=(250,255,250,255,250,255), **(utils.attr_get(node, ['width','height'])))
elif node.tag=='spacer':
if node.get('width'):
width = utils.unit_get(node.get('width'))
else:
width = utils.unit_get('1cm')
length = utils.unit_get(node.get('length'))
return platypus.Spacer(width=width, height=length)
elif node.tag=='section':
return self.render(node)
elif node.tag == 'pageNumberReset':
return PageReset()
elif node.tag in ('pageBreak', 'nextPage'):
return platypus.PageBreak()
elif node.tag=='condPageBreak':
return platypus.CondPageBreak(**(utils.attr_get(node, ['height'])))
elif node.tag=='setNextTemplate':
return platypus.NextPageTemplate(str(node.get('name')))
elif node.tag=='nextFrame':
return platypus.CondPageBreak(1000) # TODO: change the 1000 !
elif node.tag == 'setNextFrame':
from reportlab.platypus.doctemplate import NextFrameFlowable
return NextFrameFlowable(str(node.get('name')))
elif node.tag == 'currentFrame':
from reportlab.platypus.doctemplate import CurrentFrameFlowable
return CurrentFrameFlowable(str(node.get('name')))
elif node.tag == 'frameEnd':
return EndFrameFlowable()
elif node.tag == 'hr':
width_hr=node.get('width') or '100%'
color_hr=node.get('color') or 'black'
thickness_hr=node.get('thickness') or 1
lineCap_hr=node.get('lineCap') or 'round'
return platypus.flowables.HRFlowable(width=width_hr,color=color.get(color_hr),thickness=float(thickness_hr),lineCap=str(lineCap_hr))
else:
sys.stderr.write('Warning: flowable not yet implemented: %s !\n' % (node.tag,))
return None
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 pre(self,txt,style=None):
if style is None:
style = self.stylesheet.Code
return self.append(platypus.Preformatted(txt,style))
def _flowable(self, node):
if node.localName=='para':
style = self.styles.para_style_get(node)
return platypus.Paragraph(
self._textual(node), style,
**(utils.getAttrsAsDict(node, [], {'bulletText':'str'})))
elif node.localName=='name':
self.styles.names[ node.getAttribute('id')] = node.getAttribute('value')
return None
elif node.localName=='xpre':
style = self.styles.para_style_get(node)
return platypus.XPreformatted(
self._textual(node), style,
**(utils.getAttrsAsDict(node, [], {'bulletText':'str','dedent':'int','frags':'int'})))
elif node.localName=='pre':
style = self.styles.para_style_get(node)
return platypus.Preformatted(
self._textual(node), style,
**(utils.getAttrsAsDict(node, [], {'bulletText':'str','dedent':'int'})))
elif node.localName=='illustration':
return self._illustration(node)
elif node.localName=='blockTable':
return self._table(node)
elif node.localName=='title':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Title']
return platypus.Paragraph(
self._textual(node), style,
**(utils.getAttrsAsDict(node, [], {'bulletText':'str'})))
elif node.localName=='h1':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading1']
return platypus.Paragraph(
self._textual(node), style,
**(utils.getAttrsAsDict(node, [], {'bulletText':'str'})))
elif node.localName=='h2':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading2']
return platypus.Paragraph(
self._textual(node), style,
**(utils.getAttrsAsDict(node, [], {'bulletText':'str'})))
elif node.localName=='h3':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading3']
return platypus.Paragraph(
self._textual(node), style,
**(utils.getAttrsAsDict(node, [], {'bulletText':'str'})))
elif node.localName=='image':
return platypus.Image(
node.getAttribute('file'), mask=(250, 255, 250, 255, 250, 255),
**(utils.getAttrsAsDict(node, ['width','height'])))
elif node.localName=='spacer':
if node.hasAttribute('width'):
width = utils.as_pt(node.getAttribute('width'))
else:
width = utils.as_pt('1cm')
length = utils.as_pt(node.getAttribute('length'))
return platypus.Spacer(width=width, height=length)
elif node.localName=='pageBreak':
return platypus.PageBreak()
elif node.localName=='condPageBreak':
return platypus.CondPageBreak(**(utils.getAttrsAsDict(node, ['height'])))
elif node.localName=='setNextTemplate':
return platypus.NextPageTemplate(str(node.getAttribute('name')))
elif node.localName=='nextFrame':
return platypus.CondPageBreak(1000) # TODO: change the 1000 !
elif barcode_codes and node.localName=='barCode':
code = barcode_codes.get(node.getAttribute('code'), Code128)
attr_types = {'barWidth': 'pt', 'barHeight': 'pt',
'fontName': 'text', 'fontSize': 'pt',
'humanReadable': 'bool'}
return code(
self._textual(node),
**utils.getAttrsAsDict(node, ['barWidth', 'barHeight'], attr_types))
else:
sys.stderr.write('Warning: flowable not yet implemented: %s !\n' % (node.localName,))
return None
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 pre(self, text):
p = pdf.Preformatted(text, style=self.styles['Code'])
self.elements.append(p)
self.styles.names[node.get('id')] = node.get('value')
return None
elif node.tag == 'xpre':
style = self.styles.para_style_get(node)
return platypus.XPreformatted(
self._textual(node), style,
**(utils.attr_get(node, [], {
'bulletText': 'str',
'dedent': 'int',
'frags': 'int'
})))
elif node.tag == 'pre':
style = self.styles.para_style_get(node)
return platypus.Preformatted(
self._textual(node), style,
**(utils.attr_get(node, [], {
'bulletText': 'str',
'dedent': 'int'
})))
elif node.tag == 'illustration':
return self._illustration(node)
elif node.tag == 'blockTable':
return self._table(node)
elif node.tag == 'title':
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Title']
return platypus.Paragraph(
self._textual(node), style,
**(utils.attr_get(node, [], {'bulletText': 'str'})))
elif re.match('^h([1-9]+[0-9]*)$', (node.tag or '')):
styles = reportlab.lib.styles.getSampleStyleSheet()
style = styles['Heading' + str(node.tag[1:])]
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)
