def getLaTeXReport(self):
table = LaTeX.ltxTable(2)
table.addRow(["Total bp: ","{:,}".format(self.totalBp)])
table.addRow(["Peak: ",str(self.peak)])
table.addRow(["Mean base coverage: ", "{:.2f}".format(self.coverage)])
table.addRow(["",""])
table.addRow(["Unique good kmers: ","{:,}".format(self.unique_gkmers)])
table.addRow(["BGI genome size estimation: ", "{:,}".format(int(round(self.bgi)))])
table.addRow(["GSE kmers/peak: ","{:,}".format(self.kmersPerPeak)])
tex = table.getText()
img = LaTeX.ltxImage(self.genSizeHistoPlot)
tex = tex + img.getText()
return tex
def getLaTeXReport(self):
txt = "\\section{Fastqc of " +self.status.replace("_"," ")+"}\n"
table = False
imgs = 0
with open(self.outputFile) as reportReader:
for line in reportReader:
if "</h2>" in line and "Summary" not in line:
txt = txt + "\\subsection*{"+re.findall(r"]\">(.*?)</h2>",line)[0]+"}\n"
# if "Basic Statistics" in line:
# smallReport = FastqSmallReport.FastqSmallReport()
# smallReport.createSmallReport([self.forward], None)
# txt = txt + smallReport.getLaTeXReport()
# txt = txt + "\\\\"
elif "<table>" in line:
xml = "<table>"
table = True
elif "</table>" in line:
xml = xml + "</table>"
table = False
domTable = minidom.parseString(xml)
ltxTable = LaTeX.ltxTable(len(domTable.firstChild.firstChild.childNodes))
noOfRows = 0
for row in domTable.firstChild.childNodes:
cols = []
noOfRows = noOfRows + 1
if noOfRows > 15:
continue
for col in row.childNodes:
cols.append(col.firstChild.nodeValue.replace("%"," percent"))
if "Filename" in cols[0]:
continue
ltxTable.addRow(cols)
txt = txt + ltxTable.getText()
if noOfRows > 15:
txt = txt + "\\\\Total length of this table is "+ str(noOfRows) + ". The table is cut after 15 rows..."
elif table == True:
xml = xml + line.strip()
elif "<img class=\"indented\"" in line:
imgs = imgs +1
img = re.findall("src=\"(.*)\" alt=",line)[0]
ltxImg = LaTeX.ltxImage(os.path.dirname(self.outputFile) + "/" + img)
txt = txt + ltxImg.getText()
if imgs % 2 == 0:
txt = txt + "\\clearpage\n"
return txt
