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, 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 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