def __init__(self, out, node, doc):
if not node.hasAttribute('pageSize'):
pageSize = (utils.unit_get('21cm'), utils.unit_get('29.7cm'))
else:
ps = [x.strip() for x in node.getAttribute('pageSize').replace(')', '').replace(
'(', '').split(',')]
pageSize = (utils.unit_get(ps[0]), utils.unit_get(ps[1]))
cm = reportlab.lib.units.cm
self.doc_tmpl = platypus.BaseDocTemplate(out, pagesize=pageSize, **utils.attr_get(node, ['leftMargin', 'rightMargin', 'topMargin', 'bottomMargin'], {
'allowSplitting': 'int', 'showBoundary': 'bool', 'title': 'str', 'author': 'str', 'rotation': 'int'}))
self.page_templates = []
self.styles = doc.styles
self.doc = doc
pts = node.getElementsByTagName('pageTemplate')
for pt in pts:
frames = []
for frame_el in pt.getElementsByTagName('frame'):
frame = platypus.Frame(
**(utils.attr_get(frame_el, ['x1', 'y1', 'width', 'height', 'leftPadding', 'rightPadding', 'bottomPadding', 'topPadding'], {'id': 'text', 'showBoundary': 'bool'})))
frames.append(frame)
gr = pt.getElementsByTagName('pageGraphics')
if len(gr):
drw = _rml_draw(gr[0], self.doc)
self.page_templates.append(platypus.PageTemplate(
frames=frames, onPage=drw.render, **utils.attr_get(pt, [], {'id': 'str'})))
else:
self.page_templates.append(
platypus.PageTemplate(frames=frames, **utils.attr_get(pt, [], {'id': 'str'})))
self.doc_tmpl.addPageTemplates(self.page_templates)
def customer_PDF(name="form_letter.pdf"):
ladderDoc = MultiPageDocument(filename=name,
pagesize=A4,
rightMargin=72,
leftMargin=72,
topMargin=72,
bottomMargin=18,
showBoundary=0,
allowSplitting=1,
_pageBreakQuick=0)
address_header_frame = platypus.Frame(A4[0] - 4 * inch,
A4[1] - 4 * inch - 2.1 * inch,
3 * inch,
4 * inch + 1.5 * inch,
showBoundary=False)
document_reference_frame = platypus.Frame(1 * cm,
23 * cm,
A4[0] - 2 * cm,
5 * cm,
showBoundary=True)
# left_header_frame2 = platypus.Frame(1*cm,23*cm, 7.5*cm, 1*cm,showBoundary=False,leftPadding=0, bottomPadding=0,rightPadding=0, topPadding=0)
# header2_frame_right = platypus.Frame(12*cm,23*cm, 7.5*cm, 1*cm,showBoundary=True)
body_frame = platypus.Frame(1 * cm,
3 * cm,
A4[0] - 2 * cm,
21 * cm,
id='body',
showBoundary=False)
page_template = platypus.PageTemplate(
id='First',
frames=[address_header_frame, body_frame],
onPage=simple_customer_background)
body_frame = platypus.Frame(1 * cm,
3 * cm,
A4[0] - 2 * cm,
21 * cm,
id='body',
showBoundary=False)
page_template2 = platypus.PageTemplate(id='Later',
frames=[body_frame],
onPage=simple_customer_background)
ladderDoc.addPageTemplates([page_template, page_template2])
return ladderDoc
def build(self,
flowables,
onTitle=_do_nothing,
onPortrait=_do_nothing,
onLandscape=_do_nothing,
canvasmaker=canvas.Canvas):
# Recalculate in case we changed margins, sizes, etc
self._calc()
# Portrait frame
frame_portrait = p.Frame(self.leftMargin,
self.bottomMargin,
self.width,
self.height,
id='portraitFrame')
# Landscape frame
frame_landscape = p.Frame(0.75 * u.inch,
0.5 * u.inch,
9.5 * u.inch,
7.4 * u.inch,
id='landscapeFrame')
# Add page templates to this document template
self.addPageTemplates([
p.PageTemplate(id='title',
frames=frame_portrait,
onPage=onTitle,
pagesize=pagesizes.portrait(pagesizes.letter)),
p.PageTemplate(id='portrait',
frames=frame_portrait,
onPage=onPortrait,
pagesize=pagesizes.portrait(pagesizes.letter)),
p.PageTemplate(id='landscape',
frames=frame_landscape,
onPage=onLandscape,
pagesize=pagesizes.landscape(pagesizes.letter))
])
if onTitle is _do_nothing and hasattr(self, 'onTitle'):
self.pageTemplates[0].beforeDrawPage = self.onTitle
if onPortrait is _do_nothing and hasattr(self, 'onPortrait'):
self.pageTemplates[1].beforeDrawPage = self.onPortrait
if onLandscape is _do_nothing and hasattr(self, 'onLandscape'):
self.pageTemplates[2].beforeDrawPage = self.onLandscape
# Use the base class to call build
p.BaseDocTemplate.build(self, flowables, canvasmaker=canvasmaker)
def create_doc(frame_num):
doc = BaseDocTemplate(
'medium_highlights.pdf',
pagesize=A4,
topMargin=1*inch,
bottomMargin=1*inch,
leftMargin=0.5*inch,
rightMargin=0.5*inch)
frameCount = frame_num
frameWidth = (doc.width- 0.1*inch) / frameCount
frameHeight = doc.height - 0.05*inch
frame_list = [
Frame(
x1=doc.leftMargin,
y1=doc.bottomMargin,
width=frameWidth,
height=frameHeight),
Frame(
x1=doc.leftMargin + frameWidth + 0.1*inch,
y1=doc.bottomMargin,
width=frameWidth,
height=frameHeight),
]
template = platypus.PageTemplate(frames=frame_list)
doc.addPageTemplates(template)
return doc
def init_layout(self):
self.unit = reportlab.lib.units.inch
self.init_fonts()
self.init_styles()
self.document = platypus.BaseDocTemplate(self.file_name, \
pagesize=reportlab.lib.pagesizes.A4, leftMargin=20, \
rightMargin=20, topMargin=40, bottomMargin=10, \
allowSplitting=0, title=self.get_title(), \
author="Kunnafoni")
frameCount = 2
frameWidth = self.document.width / frameCount
frameHeight = self.document.height - .05 * self.unit
frames = []
#construct a frame for each column
for frame in range(frameCount):
leftMargin = self.document.leftMargin + frame * frameWidth
column = platypus.Frame(leftMargin, self.document.bottomMargin, \
frameWidth, frameHeight)
frames.append(column)
template = platypus.PageTemplate(frames=frames, onPage=self.addHeader)
self.document.addPageTemplates(template)
def setup_document(self,
file,
mode=('column', 1),
size='default',
pagesize='letter',
pagemode='portrait',
left_margin=inch,
right_margin=inch,
top_margin=inch,
bottom_margin=inch,
base_font_size=10):
frames = self.setup_frames(mode, size, pagesize, pagemode, left_margin,
right_margin, top_margin, bottom_margin,
base_font_size)
pt = platypus.PageTemplate(frames=frames)
self.doc = platypus.BaseDocTemplate(
file,
pagesize=self.pagesize,
pageTemplates=[pt],
)
self.doc.frame_width = frames[0].width
self.doc.frame_height = frames[0].height
self.styleSheet = styles.getSampleStyleSheet()
perc_scale = float(base_font_size) / self.styleSheet['Normal'].fontSize
if perc_scale != 1.0:
self.scale_stylesheet(perc_scale)
self.txt = []
def changing_headers_PDF(name="form_letter.pdf"):
ladderDoc = platypus.BaseDocTemplate(filename=name,
pagesize=A4,
rightMargin=72,
leftMargin=72,
topMargin=72,
bottomMargin=18,
showBoundary=0)
margin = 0.2 * inch
header_frame = platypus.Frame(margin, A4[1] - 0.15 * inch - margin,
A4[0] - 0.4 * inch, 1.2 * inch)
subheader_frame = platypus.Frame(
margin, A4[1] - 0.15 * inch - margin - 0.45 * inch, A4[0] - 0.4 * inch,
1.2 * inch)
body_frame = platypus.Frame(0.2 * inch, 0.2 * inch, A4[0] - 0.4 * inch,
A4[1] - 1.2 * inch)
page_template = platypus.PageTemplate(
id='begin_section',
frames=[header_frame, subheader_frame, body_frame],
onPage=simple_background)
# page_template_content = platypus.PageTemplate(id='content',frames=[body_frame],onPage=simple_background)
ladderDoc.addPageTemplates(page_template)
# ladderDoc.addPageTemplates([page_template,page_template_content])
return ladderDoc
def __init__(self, localcontext, out, node, doc, images=None, path='.',
title=None, page_limit=None):
if localcontext is None:
localcontext={'internal_header':True}
self.localcontext = localcontext
if images is None:
self.images = {}
else:
self.images = images
self.path = path
self.title = title
self.page_limit = page_limit
if not node.get('pageSize'):
pageSize = (utils.unit_get('21cm'), utils.unit_get('29.7cm'))
else:
ps = map(lambda x:x.strip(), node.get('pageSize').replace(')', '').replace('(', '').split(','))
pageSize = ( utils.unit_get(ps[0]),utils.unit_get(ps[1]) )
self.doc_tmpl = TinyDocTemplate(out, pagesize=pageSize, **utils.attr_get(node, ['leftMargin','rightMargin','topMargin','bottomMargin'], {'allowSplitting':'int','showBoundary':'bool','rotation':'int','title':'str','author':'str'}))
if self.page_limit is not None:
self.doc_tmpl.set_page_limit(self.page_limit)
self.page_templates = []
self.styles = doc.styles
self.doc = doc
self.image=[]
pts = node.findall('pageTemplate')
for pt in pts:
frames = []
for frame_el in pt.findall('frame'):
frame = platypus.Frame( **(utils.attr_get(frame_el, ['x1','y1', 'width','height', 'leftPadding', 'rightPadding', 'bottomPadding', 'topPadding'], {'id':'str', 'showBoundary':'bool'})) )
if utils.attr_get(frame_el, ['last']):
frame.lastFrame = True
frames.append( frame )
try :
gr = pt.findall('pageGraphics')\
or pt[1].findall('pageGraphics')
except Exception: # FIXME: be even more specific, perhaps?
gr=''
if len(gr):
# self.image=[ n for n in utils._child_get(gr[0], self) if n.tag=='image' or not self.localcontext]
drw = _rml_draw(self.localcontext,gr[0], self.doc, images=images, path=self.path, title=self.title)
self.page_templates.append( platypus.PageTemplate(frames=frames, onPage=drw.render, **utils.attr_get(pt, [], {'id':'str'}) ))
else:
drw = _rml_draw(self.localcontext,node,self.doc,title=self.title)
self.page_templates.append( platypus.PageTemplate(frames=frames,onPage=drw.render, **utils.attr_get(pt, [], {'id':'str'}) ))
self.doc_tmpl.addPageTemplates(self.page_templates)
def letter_PDF(name="form_letter.pdf"):
ladderDoc = platypus.BaseDocTemplate(filename=name,
pagesize=A4,
rightMargin=72,
leftMargin=72,
topMargin=72,
bottomMargin=18,
showBoundary=0,
allowSplitting=0,
_pageBreakQuick=0)
address_header_frame = platypus.Frame(A4[0] - 4 * inch,
A4[1] - 4 * inch - 2.1 * inch,
3 * inch,
4 * inch + 1.5 * inch,
showBoundary=False)
left_header_frame2 = platypus.Frame(1 * cm,
23 * cm,
7.5 * cm,
1 * cm,
showBoundary=False,
leftPadding=0,
bottomPadding=0,
rightPadding=0,
topPadding=0)
header2_frame_right = platypus.Frame(12 * cm,
23 * cm,
7.5 * cm,
1 * cm,
showBoundary=False)
body_frame = platypus.Frame(1 * cm,
6 * cm,
A4[0] - 2 * cm, (17 - 1) * cm,
showBoundary=False)
bottom_left_frame = platypus.Frame(1 * cm,
3 * cm, (A4[0] - 2 * cm) / 2,
5 * cm,
showBoundary=False)
bottom_right_frame = platypus.Frame(1 * cm + (A4[0] - 2 * cm) / 2,
3 * cm, (A4[0] - 2 * cm) / 2,
5 * cm,
showBoundary=False)
page_template = platypus.PageTemplate(id='AllPages',
frames=[
address_header_frame,
left_header_frame2,
header2_frame_right, body_frame,
bottom_left_frame,
bottom_right_frame
],
onPage=simple_customer_background)
ladderDoc.addPageTemplates([page_template])
return ladderDoc
def __init__(self, localcontext, out, node, doc, images=None, path='.', title=None):
if images is None:
images = {}
if not localcontext:
localcontext={'internal_header':True}
self.localcontext = localcontext
self.images= images
self.path = path
self.title = title
pagesize_map = {'a4': A4,
'us_letter': letter
}
pageSize = (841.8897637795275, 595.275590551181)
self.doc_tmpl = TinyDocTemplate(out, pagesize=pageSize, **utils.attr_get(node, ['leftMargin','rightMargin','topMargin','bottomMargin'], {'allowSplitting':'int','showBoundary':'bool','rotation':'int','title':'str','author':'str'}))
self.page_templates = []
self.styles = doc.styles
self.doc = doc
self.image=[]
pts = node.findall('pageTemplate')
for pt in pts:
frames = []
for frame_el in pt.findall('frame'):
frame = platypus.Frame( **(utils.attr_get(frame_el, ['x1','y1', 'width','height', 'leftPadding', 'rightPadding', 'bottomPadding', 'topPadding'], {'id':'str', 'showBoundary':'bool'})) )
if utils.attr_get(frame_el, ['last']):
frame.lastFrame = True
frames.append( frame )
try :
gr = pt.findall('pageGraphics')\
or pt[1].findall('pageGraphics')
except Exception: # FIXME: be even more specific, perhaps?
gr=''
if len(gr):
# self.image=[ n for n in utils._child_get(gr[0], self) if n.tag=='image' or not self.localcontext]
drw = _rml_draw(self.localcontext,gr[0], self.doc, images=images, path=self.path, title=self.title)
self.page_templates.append( platypus.PageTemplate(frames=frames, onPage=drw.render, **utils.attr_get(pt, [], {'id':'str'}) ))
else:
drw = _rml_draw(self.localcontext,node,self.doc,title=self.title)
self.page_templates.append( platypus.PageTemplate(frames=frames,onPage=drw.render, **utils.attr_get(pt, [], {'id':'str'}) ))
self.doc_tmpl.addPageTemplates(self.page_templates)
def process(self):
args = dict(self.getAttributeValues(attrMapping=self.attrMapping))
pagesize = args.pop('pagesize', None)
self.frames = []
self.pt = platypus.PageTemplate(**args)
self.processSubDirectives()
self.pt.frames = self.frames
if pagesize:
self.pt.pagesize = pagesize
self.parent.parent.doc.addPageTemplates(self.pt)
def start_PDF(name="form_letter.pdf"):
ladderDoc = platypus.BaseDocTemplate(filename=name,
pagesize=A4,
rightMargin=72,
leftMargin=72,
topMargin=72,
bottomMargin=18,
showBoundary=0)
body_frame = platypus.Frame(0.2 * inch, 0.2 * inch, A4[0] - 0.4 * inch,
A4[1] - 1.2 * inch)
page_template = platypus.PageTemplate(id='AllPages',
frames=[body_frame],
onPage=funcy)
ladderDoc.addPageTemplates([page_template])
return ladderDoc
def __init__(self, filename):
frame = platypus.Frame(20 * mm,
20 * mm,
170 * mm,
227 * mm,
showBoundary=0,
topPadding=0,
bottomPadding=0,
leftPadding=0,
rightPadding=0)
page = platypus.PageTemplate("main",
frames=[frame],
onPage=self._decorate_page)
self.doc = platypus.BaseDocTemplate(filename, pageTemplates=[page])
self.story = []
self.address = None
def basic_PDF(name="form_letter.pdf", body_frame=None):
ladderDoc = platypus.BaseDocTemplate(filename=name,
pagesize=A4,
rightMargin=72,
leftMargin=72,
topMargin=72,
bottomMargin=18,
showBoundary=0)
if not body_frame:
body_frame = platypus.Frame(0.2 * inch, 0.2 * inch, A4[0] - 0.4 * inch,
A4[1] - 1.2 * inch)
else:
mainlog.debug("Using given body frame : {}".format(body_frame))
page_template = platypus.PageTemplate(id='AllPages',
frames=[body_frame],
onPage=simple_background)
ladderDoc.addPageTemplates([page_template])
return ladderDoc
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 prepareReport(self, session):
#this is the report lab set up stuff
OutputElements = []
output = platypus.BaseDocTemplate('/tmp/temp.pdf')
#A4 page size setup with margins
output.pagesize = (8.3 * inch, 11.7 * inch)
output.leftMargin = 0.5 * inch
output.rightMargin = 0.5 * inch
output.topMargin = 0.5 * inch
output.bottomMargin = 0.5 * inch
output.width = output.pagesize[
0] - output.leftMargin - output.rightMargin
output.height = output.pagesize[
1] - output.topMargin - output.bottomMargin
if self.columns == 1:
#set up the columns
interFrameMargin = 0.5 * inch
frameWidth = output.width / 2 - interFrameMargin / 2
frameHeight = output.height - inch * 0.6
framePadding = 0 * inch
# create a frameset called withHeader
withHeader = []
# append header settings and 2 columns
leftMargin = output.leftMargin
titlebar = platypus.Frame(leftMargin,
output.height,
output.width,
0.75 * inch,
leftPadding=0,
rightPadding=0,
topPadding=0,
bottomPadding=0,
showBoundary=0)
withHeader.append(titlebar)
column = platypus.Frame(leftMargin, output.bottomMargin,
frameWidth, frameHeight)
withHeader.append(column)
leftMargin = output.leftMargin + frameWidth + interFrameMargin
column = platypus.Frame(leftMargin, output.bottomMargin,
frameWidth, frameHeight)
withHeader.append(column)
#create frameset called withoutHeader
withoutHeader = []
#change the frame height because no header here
frameHeight = output.height - inch * 0.2
#add two columns
leftMargin = output.leftMargin
column = platypus.Frame(leftMargin, output.bottomMargin,
frameWidth, frameHeight)
withoutHeader.append(column)
leftMargin = output.leftMargin + frameWidth + interFrameMargin
column = platypus.Frame(leftMargin, output.bottomMargin,
frameWidth, frameHeight)
withoutHeader.append(column)
else:
#set up the full page stuff
frameWidth = output.width
frameHeight = output.height - inch * 0.6
framePadding = 0 * inch
withHeader = []
#append header and single column (full page)
leftMargin = output.leftMargin
titlebar = platypus.Frame(leftMargin,
output.height,
output.width,
0.75 * inch,
leftPadding=0,
rightPadding=0,
topPadding=0,
bottomPadding=0,
showBoundary=0)
withHeader.append(titlebar)
column = platypus.Frame(leftMargin, output.bottomMargin,
frameWidth, frameHeight)
withHeader.append(column)
withoutHeader = []
frameHeight = output.height - inch * 0.2
column = platypus.Frame(leftMargin, output.bottomMargin,
frameWidth, frameHeight)
withoutHeader.append(column)
def header(Elements, txt, style=HeaderStyle):
s = platypus.Spacer(0.2 * inch, 0.2 * inch)
Elements.append(s)
style.alignment = 1
style.fontName = self.psfont
style.fontSize = 18
style.borderWidth = 0
para = platypus.Paragraph(txt, style)
Elements.append(para)
headerPage = platypus.PageTemplate(id='Header', frames=withHeader)
normalPage = platypus.PageTemplate(id='noHeader', frames=withoutHeader)
if self.headerString is not None:
output.addPageTemplates([headerPage, normalPage])
header(OutputElements, self.headerString)
OutputElements.append(platypus.FrameBreak())
else:
output.addPageTemplates([normalPage])
OutputElements.extend(self.getData(session))
#numbered canvas does footer (including page numbers and date is requested)
NumberedCanvas.setFooterText(self.footerString)
output.build(OutputElements, canvasmaker=NumberedCanvas)
output.showBoundary = True
fileInput = open('/tmp/temp.pdf', 'r')
doc = StringDocument(fileInput.read())
os.remove('/tmp/temp.pdf')
yield doc
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)
