def get_fastqc_summary(self):
stats = {}
for stat_line in self._fastqc_data_section("Basic Statistics")[1:]:
k, v = [safe_latex(x) for x in stat_line.split("\t")[:2]]
stats[k] = v
over_rep = []
for line in self._fastqc_data_section("Overrepresented sequences")[1:]:
parts = [safe_latex(x) for x in line.split("\t")]
over_rep.append(parts)
over_rep[-1][0] = self._splitseq(over_rep[-1][0])
return stats, over_rep[:self._max_overrep]
def generate_report(self, name=None, summary=None, figures=None,
overrep=None):
template = Template(self._template)
safe_name = safe_latex(name)
section = template.render(name=safe_name, summary=summary,
summary_table=summary, figures=figures,
overrep=overrep)
return section
def generate_report(self, name=None, summary=None, figures=None,
overrep=None):
template = Template(self._template)
safe_name = safe_latex(name)
section = template.render(name=safe_name, summary=summary,
summary_table=summary, figures=figures,
overrep=overrep)
return section
def generate_report(self, name, figures=None):
template = Template(self._template)
clean_name = safe_latex(name)
#clean_figures = self.clean_figures(figures)
#section = template.render(name=clean_name, figures=clean_figures)
clean_figures = [(remove_suffix(figure[0]), figure[1], figure[2])
for figure in figures]
section = template.render(name=clean_name, figures=clean_figures)
return section
def get_fastqc_summary(self):
stats = {}
for stat_line in self._fastqc_data_section("Basic Statistics")[1:]:
k, v = [safe_latex(x) for x in stat_line.split("\t")[:2]]
stats[k] = v
over_rep = []
for line in self._fastqc_data_section("Overrepresented sequences")[1:]:
parts = [safe_latex(x) for x in line.split("\t")]
over_rep.append(parts)
over_rep[-1][0] = self._splitseq(over_rep[-1][0])
return stats, over_rep[:self._max_overrep]
pieces = []
cur_piece = []
for s in seq:
if len(cur_piece) >= self._max_seq_size:
pieces.append("".join(cur_piece))
cur_piece = []
cur_piece.append(s)
pieces.append("".join(cur_piece))
return " ".join(pieces)
def get_fastqc_summary(self):
stats = {}
for stat_line in self._fastqc_data_section("Basic Statistics")[1:]:
k, v = [safe_latex(x) for x in stat_line.split("\t")[:2]]
stats[k] = v
over_rep = []
for line in self._fastqc_data_section("Overrepresented sequences")[1:]:
parts = [safe_latex(x) for x in line.split("\t")]
over_rep.append(parts)
over_rep[-1][0] = self._splitseq(over_rep[-1][0])
return stats, over_rep[:self._max_overrep]
pieces = []
cur_piece = []
for s in seq:
if len(cur_piece) >= self._max_seq_size:
pieces.append("".join(cur_piece))
cur_piece = []
cur_piece.append(s)
pieces.append("".join(cur_piece))
return " ".join(pieces)
def clean_figures(self, figures):
new_figures = []
for figure in figures:
filename = safe_latex(figure[0])
new_figures.append((filename, figure[1], figure[2]))
return new_figures
