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 = ""
table = LaTeX.ltxTable(len(self.fastqInfo.values()[0]) + 1)
table.addRow(
[
"Fastq file",
"Total bases",
"number of reads",
"AVG read length",
"Percentage high quality bases ($qv > 30$)",
]
)
for [index, fastqEntry] in self.fastqInfo.iteritems():
table.addRow([index] + fastqEntry)
txt = txt + table.getText()
return txt + "\\\\"
def getLaTeXReport(self):
"""
Convert all previously calculated statistics into LaTeX with this method.
"""
txt = "\\subsection{Statistics}\n"
table = LaTeX.ltxTable(2)
table.addRow(["Total sequences: ",str(self.totalSeqs)])
table.addRow(["Total length: ","{:,}".format(self.totalLen)])
table.addRow(["GC perc: ","{:.2f}".format(self.gcPerc) + "\%"])
table.addRow(["Longest sequence: ","{:,}".format(self.longestSeq)])
table.addRow(["N50 index: ","{:,}".format(self.n50Index)])
table.addRow(["N50: ","{:,}".format(self.n50)])
table.addRow(["",""])
table.addRow(["N90 index: ","{:,}".format(self.n90Index)])
table.addRow(["N90: ","{:,}".format(self.n90)])
if hasattr(self, "cegmaScore"):
table.addRow(["",""])
table.addRow(["Cegma complete: ",self.cegmaScore[0] + "\%"])
table.addRow(["Cegma partial: ",self.cegmaScore[1] + "\%"])
for name, value in self.otherCegmaScores.iteritems():
table.addRow(["",""])
print value[0]
table.addRow([name + " complete: ",value[0] + "\%"])
table.addRow([name + " partial: ",value[1] + "\%"])
if hasattr(self, "rawDnaMappingStats"):
table.addRow(["",""])
table.addRow(["DNA reads: ","{:,}".format(int(self.rawDnaMappingStats["total"]))])
table.addRow(["Mapped: ",self.rawDnaMappingStats["mapped"] + "\%"])
if "propPair" in self.rawDnaMappingStats:
table.addRow(["Properly paired",self.rawDnaMappingStats["propPair"] + "\%"])
table.addRow(["Error rate: ","{:.2f}".format(self.errorRate) + " SNPs per 10kb"])
table.addRow(["SNP density: ","{:.2f}".format(self.snpDensity) + " SNPs per 10kb"])
if hasattr(self, "rnaMappingStats"):
table.addRow(["",""])
table.addRow(["RNA reads: ","{:,}".format(int(self.rnaMappingStats["total"]))])
table.addRow(["Mapped: ",self.rnaMappingStats["mapped"] + "\%"])
if "propPair" in self.rnaMappingStats:
table.addRow(["Properly paired: ",self.rnaMappingStats["propPair"] + "\%"])
txt = txt + table.getText()
txt = txt + "\\begin{figure}[h]\n"
txt = txt + "\\includegraphics[scale=0.7]{" + self.a50Plot + "}\n"
txt = txt + "\\end{figure}\n"
return txt
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