def run(self, vectorHtml=None):
""" Run Lane HTML Documentation Building
vectorHtml - vector of html tags
"""
#1. Add HTML Report Header
self.addHtmlReportHeader(vectorHtml)
vectorHtml.append(
'<H1 id="title"> <U> Methylation Pipeline Report Project %s </U> </H1>'
% (self.name_project))
vector_sample_links = []
for sampleStats in self.vector_samples:
sampleHtml = "%s/%s.html" % (self.output_dir, sampleStats.name)
isizeHistogram = "%s/%s.isize.png" % (os.path.dirname(
self.output_dir), sampleStats.name)
png_mapq_histogram = "%s/%s.mapq.png" % (os.path.dirname(
self.output_dir), sampleStats.name)
sampleReport = SampleHtml(project_name=self.name_project,sample_stats=sampleStats,html_parent_path=self.project_html_document,\
html_sample=sampleHtml,png_insert_size_histogram=isizeHistogram,png_mapq_histogram=png_mapq_histogram)
vSampleHtml = []
sampleReport.run(vSampleHtml)
RunBasicStats.saveDocument(file_name=sampleHtml,
vectorContent=vSampleHtml)
vector_sample_links.append(os.path.basename(sampleHtml))
#3.Links table
self.createLinksSumupSampleTables(vector_html=vectorHtml,
vector_links=vector_sample_links,
samplesStats=self.vector_samples)
#4.Close Html
self.closeHtmlReport(vectorHtml=vectorHtml)
def __init__(self,
mapping_stats=None,
png_mapq_histogram=None,
png_insert_size_histogram=None):
#Call Parent class constructor
#super(RunBasicStats, self).__init__()
RunBasicStats.__init__(
self,
mapping_stats=mapping_stats,
png_mapq_histogram=png_mapq_histogram,
png_insert_size_histogram=png_insert_size_histogram)
def run(self, vectorSphinx=None):
""" Run Sumup Sphinx Documentation Building
vectorSphinx - vector of html tags
"""
#1. Add SPHINX Report Header
#Scaped name
scaped_name = ""
for character in self.name_project:
if character == "_":
scaped_name += "\\%s" % (character)
else:
scaped_name += "%s" % (character)
self.addPartLine(
ident=0,
vectorSphinx=vectorSphinx,
title="CpG Report from Methylation Pipeline Project %s" %
(scaped_name))
vectorDocuments = []
vectorDocuments.append("SUMUP")
#2. Create Sample and lanes Report
for sample, stats in sorted(self.dictionary_samples.iteritems()):
sampleSphinx = "%s/%s.rst" % (self.output_dir, sample)
vectorDocuments.append("%s" % (sample))
#Create Build SPHINX
vector_sphinx = []
sphinxReport = SphinxCpgsReport()
sphinxReport.run(vectorSphinx=vector_sphinx,
ident=0,
lenCell=30,
cpgStats=stats,
output_dir=self.output_dir,
name=sample)
#Store Sphinx file
RunBasicStats.saveDocument(file_name=sampleSphinx,
vectorContent=vector_sphinx)
#3.Toc Table
vectorSphinx.append("\n")
self.addTocTree(vectorSphinx=vectorSphinx,
vectorDocuments=vectorDocuments)
def buildSphinxCpgReport(inputs=None, output_dir=None, name=None):
""" Build Sphinx Variant report
inputs -- dictionary of samples and json stats {"sample":"stats_cpg.json,meth_values_cpg.json"}
output_dir -- Output directory to store html documents.
name -- Name basic to build output results.
"""
#Check output directory
if not os.path.exists("%s/IMG/" % (output_dir)):
os.makedirs("%s/IMG/" % (output_dir))
#Dictionary Samples CpgStats {"sample":"stats_cpg.json"}
dict_samples_cpg = {}
for sample, json_files in inputs.iteritems():
#CpgStats object
cpgStats = CpgStats()
#Json Parsing
with open(json_files[0], 'r') as file_json:
with open(json_files[1], 'r') as meth_json:
cpgStats.update(dictionary=json.load(file_json),
methDict=json.load(meth_json))
#Update directory of samples
dict_samples_cpg[sample] = cpgStats
#SumupSphinx object
vector_sumup_sphinx = []
sumupCpgSphinx = SumupCpgSphinx(output_dir=output_dir,
name_project=name,
dictionary_samples=dict_samples_cpg)
sumupCpgSphinx.run(vectorSphinx=vector_sumup_sphinx)
RunBasicStats.saveDocument(file_name=sumupCpgSphinx.cpg_sphinx_document,
vectorContent=vector_sumup_sphinx)
#Config python file
cfgFile = ConfigSphinx(path_config_file="%s/conf.py" % (output_dir),
path_makefile_file="%s/Makefile" % (output_dir),
master_file=name,
project_name=name,
main_title='CPGs REPORT')
cfgFile.run()
def buildCpgReport(inputs=None, output_dir=None, name=None):
""" Build CpG report.
inputs -- dictionary of samples and json stats {"sample":"stats_cpg.json,meth_values_cpg.json"}
output_dir -- Output directory to store html documents.
name -- Name basic to build output results.
"""
#Check output directory
if not os.path.exists("%s/IMG/" % (output_dir)):
os.makedirs("%s/IMG/" % (output_dir))
#Dictionary Samples CpgStats {"sample":"stats_cpg.json"}
dict_samples_cpg = {}
for sample, json_files in inputs.iteritems():
#CpgStats object
cpgStats = CpgStats()
#Json Parsing
with open(json_files[0], 'r') as file_json:
with open(json_files[1], 'r') as meth_json:
cpgStats.update(dictionary=json.load(file_json),
methDict=json.load(meth_json))
#Update directory of samples
dict_samples_cpg[sample] = cpgStats
#IndexHtml object
vector_index_html = []
indexCpgHtml = IndexCpgHtml(output_dir=output_dir,
name_project=name,
dictionary_samples=dict_samples_cpg)
indexCpgHtml.run(vectorHtml=vector_index_html)
RunBasicStats.saveDocument(file_name=indexCpgHtml.cpg_html_document,
vectorContent=vector_index_html)
#CSS object
cssBuilder = BasicHtml()
vector_css = []
cssBuilder.buildStyleSheet(vector_css)
RunBasicStats.saveDocument(file_name="%s/style.css" % (output_dir),
vectorContent=vector_css)
def buildReport(inputs=None, output_dir=None, name=None, ref_length=""):
""" Build report per lane and sample.
inputs -- Dictionary of samples and lanes [sample][fli]json_file
output_dir -- Output directory to store html documents.
name -- Name basic to build output results.
ref_length -- Length of the reference
"""
#Check output directory
if not os.path.exists(output_dir):
os.makedirs(output_dir)
#Proces list Lane files
vector_samples = []
for sample, fli_json in inputs.iteritems():
list_stats_lanes = []
for fli, json_files in fli_json.iteritems():
for json_file in json_files:
lane = LaneStats(name=fli,
json_file=json_file,
ref_length=int(ref_length))
list_stats_lanes.append(lane)
vector_samples.append(
SampleStats(name=sample, list_lane_stats=list_stats_lanes))
#IndexHtml object
vector_index_html = []
indexHtml = IndexHtml(output_dir=output_dir,
name_project=name,
vector_samples=vector_samples)
indexHtml.run(vectorHtml=vector_index_html)
RunBasicStats.saveDocument(file_name=indexHtml.project_html_document,
vectorContent=vector_index_html)
#CSS object
cssBuilder = BasicHtml()
vector_css = []
cssBuilder.buildStyleSheet(vector_css)
RunBasicStats.saveDocument(file_name="%s/style.css" % (output_dir),
vectorContent=vector_css)
def run(self, vectorHtml=None):
""" Run Lane HTML Documentation Building
vectorHtml - vector of html tags
"""
#1. Add HTML Report Header
self.addHtmlReportHeader(vectorHtml)
vectorHtml.append(
'<H1 id="title"> <U> CpG Report from Methylation Pipeline Project %s </U> </H1>'
% (self.name_project))
vector_sample_links = []
for sample, stats in sorted(self.dictionary_samples.iteritems()):
sampleHtml = "%s/%s_cpg.html" % (self.output_dir, sample)
#Create Build HTML
vSampleHtml = []
sampleCpgReport = HtmlCpgReport()
sampleCpgReport.run(vectorHtml=vSampleHtml,
cpgStats=stats,
output_dir=self.output_dir,
name=sample,
parentName=self.name_project,
parentDocument=self.cpg_html_document)
self.closeHtmlReport(vectorHtml=vSampleHtml)
RunBasicStats.saveDocument(file_name=sampleHtml,
vectorContent=vSampleHtml)
vector_sample_links.append([os.path.basename(sampleHtml), sample])
#2.Links table
self.createLinksTables(vector_html=vectorHtml,
vector_links=vector_sample_links,
title="Sample Reports",
color="blue")
#3.Close Html
self.closeHtmlReport(vectorHtml=vectorHtml)
def buildSphinxVariantReport(inputs=None, output_dir=None, name=None):
""" Build Sphinx Variant report
inputs -- List of json files
output_dir -- Output directory to store html documents.
name -- Name basic to build output results.
"""
#Check output directory
if not os.path.exists("%s/IMG/" % (output_dir)):
os.makedirs("%s/IMG/" % (output_dir))
#Proces list chromosome files
dict_samples = {}
for sample, chrom_json_files in inputs.iteritems():
#Parsing json file
basicStats = VariantStats()
q20BasicStats = VariantStats()
coverageStats = VariantStats()
genotypeQualityStats = VariantStats()
mutationChangesStats = VariantStats()
mutationChangesQ20Stats = VariantStats()
chromosomeStats = VariantStats()
#Load al json files
for json_file in chrom_json_files:
with open(json_file, 'r') as file_json:
data = json.load(file_json)
basicStats.addValues({
"Total Snps":
data["TotalSnps"],
"Total indels":
data["TotalIndels"],
"Total Multiallelic":
data["TotalMultiallelic"]
})
q20BasicStats.addValues({
"Q>20 Snps":
data["q20Snps"],
"Q>20 indels":
data["q20Indels"],
"Q>20 Multiallelic":
data["q20Multiallelic"]
})
coverageStats.addValues(data["coverageVariants"])
genotypeQualityStats.addValues(data["qualityVariants"])
mutationChangesStats.addValues(data["mutations"])
mutationChangesQ20Stats.addValues(data["mutationsQ20"])
chromosomeStats.addValues(data["chromosomeVariants"])
#Create Build HTML
dict_samples[sample] = [
basicStats, q20BasicStats, coverageStats, genotypeQualityStats,
mutationChangesStats, mutationChangesQ20Stats, chromosomeStats
]
#SumupSphinx object
vector_sumup_sphinx = []
sumupVariantsSphinx = SumupVariantsSphinx(output_dir=output_dir,
name_project=name,
dictionary_samples=dict_samples)
sumupVariantsSphinx.run(vectorSphinx=vector_sumup_sphinx)
RunBasicStats.saveDocument(
file_name=sumupVariantsSphinx.variants_sphinx_document,
vectorContent=vector_sumup_sphinx)
#Config python file
cfgFile = ConfigSphinx(path_config_file="%s/conf.py" % (output_dir),
path_makefile_file="%s/Makefile" % (output_dir),
master_file=name,
project_name=name,
main_title='VARIANTS REPORT')
cfgFile.run()
def buildVariantReport(inputs=None, output_dir=None, name=None):
""" Build variant report.
inputs -- Dictionary of samples and list of files. [sample] [barcode_chrN.json,barcode_chrN+1.json]
output_dir -- Output directory to store html documents.
name -- Name basic to build output results.
"""
#Check output directory
if not os.path.exists("%s/IMG/" % (output_dir)):
os.makedirs("%s/IMG/" % (output_dir))
#Proces list chromosome files
dict_samples = {}
for sample, chrom_json_files in inputs.iteritems():
#Parsing json file
basicStats = VariantStats()
q20BasicStats = VariantStats()
coverageStats = VariantStats()
genotypeQualityStats = VariantStats()
mutationChangesStats = VariantStats()
mutationChangesQ20Stats = VariantStats()
chromosomeStats = VariantStats()
#Load al json files
for json_file in chrom_json_files:
with open(json_file, 'r') as file_json:
data = json.load(file_json)
basicStats.addValues({
"Total Snps":
data["TotalSnps"],
"Total indels":
data["TotalIndels"],
"Total Multiallelic":
data["TotalMultiallelic"]
})
q20BasicStats.addValues({
"Q>20 Snps":
data["q20Snps"],
"Q>20 indels":
data["q20Indels"],
"Q>20 Multiallelic":
data["q20Multiallelic"]
})
coverageStats.addValues(data["coverageVariants"])
genotypeQualityStats.addValues(data["qualityVariants"])
mutationChangesStats.addValues(data["mutations"])
mutationChangesQ20Stats.addValues(data["mutationsQ20"])
chromosomeStats.addValues(data["chromosomeVariants"])
#Create Build HTML
dict_samples[sample] = [
basicStats, q20BasicStats, coverageStats, genotypeQualityStats,
mutationChangesStats, mutationChangesQ20Stats, chromosomeStats
]
#IndexHtml object
vector_index_html = []
indexVariantsHtml = IndexVariantsHtml(output_dir=output_dir,
name_project=name,
dictionary_samples=dict_samples)
indexVariantsHtml.run(vectorHtml=vector_index_html)
RunBasicStats.saveDocument(
file_name=indexVariantsHtml.variants_html_document,
vectorContent=vector_index_html)
#CSS object
cssBuilder = BasicHtml()
vector_css = []
cssBuilder.buildStyleSheet(vector_css)
RunBasicStats.saveDocument(file_name="%s/style.css" % (output_dir),
vectorContent=vector_css)
qualityNonRefCpG, plotMethylation, summaryMethylation
]
}
#Create Index BSCall Report
htmlIndexBsCall = HtmlIndexBsCall(output_dir=output_dir,
name_project=name,
samples_stats=dict_samples,
samples_summary=dict_samples_summaries)
htmlIndexBsCall.createPage()
#CSS object
cssBuilder = BasicHtml()
vector_css = []
cssBuilder.buildStyleSheet(vector_css)
RunBasicStats.saveDocument(file_name="%s/style.css" % (output_dir),
vectorContent=vector_css)
#Create Index BSCall Report
sphinxIndexBsCall = SphinxIndexBsCall(output_dir="%s/SPHINX/" %
(output_dir),
name_project=name,
samples_stats=dict_samples)
sphinxIndexBsCall.createPage()
#Config python file
cfgFile = ConfigSphinx(path_config_file="%s/SPHINX/conf.py" % (output_dir),
path_makefile_file="%s/SPHINX/Makefile" %
(output_dir),
master_file=name,
project_name=name,
main_title='BSCALL REPORT')
def run(self, vectorHtml=None):
""" Run Lane HTML Documentation Building
vectorHtml - vector of html tags
"""
#1. Add HTML Report Header
self.addHtmlStartReport(vectorHtml=vectorHtml)
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml,
title="Mapping Stats (Reads)")
vectorHtml.extend(self.createStatsTable(color='blue'))
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml,
title="Uniqueness (Fragments)")
vectorHtml.extend(
self.createUniqueFragmentsTable(
color='green',
unique_fragments=self.mapping_stats.totalSampleUniqueReads,
average_unique=self.mapping_stats.averageSampleUniqueReads))
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml,
title="Mapping Stats (Bases)")
vectorHtml.extend(self.createBasesStatsTable(color='blue'))
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml,
title="Bisulfite Conversion Rate")
vectorHtml.extend(self.createBisulfiteConversionRate(color='green'))
if self.is_paired:
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml, title="Correct Pairs")
vectorHtml.extend(
self.createSingleValueTable(
color='blue',
name='Correct Pairs',
value=self.mapping_stats.correct_pairs))
#2. Lane Stats and links per lane
vLaneLinksVector = []
for laneStats in self.mapping_stats.list_lane_stats:
htmlLane = "%s/%s.html" % (os.path.dirname(
self.html_parent_path), laneStats.name)
mapqHistogram = "%s/%s.mapq.png" % (os.path.dirname(
self.html_parent_path), laneStats.name)
isizeHistogram = "%s/%s.isize.png" % (os.path.dirname(
self.html_parent_path), laneStats.name)
vLaneHtml = []
laneHtml = LaneHtml(project_name=self.project_name,
sample_name=self.mapping_stats.name,
lane_stats=laneStats,
png_mapq_histogram=mapqHistogram,
png_insert_size_histogram=isizeHistogram,
html_parent_path=self.html_sample)
laneHtml.run(vLaneHtml)
RunBasicStats.saveDocument(file_name=htmlLane,
vectorContent=vLaneHtml)
vLaneLinksVector.append(
[laneStats.name, os.path.basename(htmlLane)])
#3.Mapping Quality
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml, title="Mapping Quality")
vectorHtml.extend(self.buildMapqHistogram(color='green'))
#4. Insert Size Plot
if self.is_paired:
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml,
title="Insert Size Plot")
vectorHtml.extend(self.buildInsertSizePlot(color='blue'))
#5.Links table
self.addSpaceSection(vectorHtml=vectorHtml)
self.addSectionTitle(vectorHtml=vectorHtml,
title="Mapping Lanes Reports")
self.createLinksTables(vectorHtml,
vLaneLinksVector,
title="LANE REPORTS",
color="green")
#6. Close html
self.closeHtmlReport(vectorHtml=vectorHtml)