def wr_xlsx(self, fout_xlsx, goea_results, **kws): """Write a xlsx file.""" prt_flds = kws['prt_flds'] if 'prt_flds' in kws else self.get_prtflds_default(goea_results) xlsx_data = self.get_nts(goea_results, prt_flds, rpt_fmt=True, **kws) if 'fld2col_widths' not in kws: kws['fld2col_widths'] = {f:self.default_fld2col_widths.get(f, 8) for f in prt_flds} RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)
def wr_xlsx(self, fout_xlsx, goea_results, **kws): """Write a xlsx file.""" # kws: prt_if indent itemid2name(study_items) prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results)) xlsx_data = get_goea_nts_prt(goea_results, prt_flds, **kws) if 'fld2col_widths' not in kws: kws['fld2col_widths'] = {f:self.default_fld2col_widths.get(f, 8) for f in prt_flds} RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)
def wr_xlsx(self, fout_xlsx, goea_results, **kws): """Write a xlsx file.""" # kws: prt_if indent prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results)) xlsx_data = get_goea_nts_prt(goea_results, prt_flds, **kws) if 'fld2col_widths' not in kws: kws['fld2col_widths'] = {f:self.default_fld2col_widths.get(f, 8) for f in prt_flds} RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)
def wr_xlsx(self, fout_xlsx): """Write counts of GO terms at all levels and depths.""" from goatools.wr_tbl import wr_xlsx kws = { 'title' : "GO Counts in {VER}".format(VER=self.obo.version), 'hdrs' :["Dep/Lev", "BP Depth", "MF Depth", "CC Depth", "BP Level", "MF Level", "CC Level"]} wr_xlsx(fout_xlsx, self.get_data(), **kws)
def wr_xlsx(self, fout_xlsx): """Write counts of GO terms at all levels and depths.""" from goatools.wr_tbl import wr_xlsx kws = { 'title' : self.title, 'hdrs' :["Dep/Lev", "BP Depth", "MF Depth", "CC Depth", "BP Level", "MF Level", "CC Level"]} wr_xlsx(fout_xlsx, self.get_data(), **kws)
def wr_xlsx(self, fout_xlsx, goea_results, **kws): """Write a xlsx file.""" # kws: prt_if indent itemid2name(study_items) objprt = PrtFmt() prt_flds = kws.get('prt_flds', self.objprtres.get_prtflds_default(goea_results)) xlsx_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws) if 'fld2col_widths' not in kws: kws['fld2col_widths'] = {f:objprt.default_fld2col_widths.get(f, 8) for f in prt_flds} RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)
def wr_xlsx(self, fout_xlsx): """Write counts of GO terms at all levels and depths.""" from goatools.wr_tbl import wr_xlsx kws = { 'title' : self.title(), 'hdrs' :["Dep/Lev", "BP Depth", "MF Depth", "CC Depth", "BP Level", "MF Level", "CC Level"]} wr_xlsx(fout_xlsx, self.get_data(), **kws)
def _wr_3fmt_wrtbl(tsv_nts, goea_results, wr_params, log): """Using functions in the wr_tbl pkg, demonstrate printing a subset of namedtuple fields.""" goea_nts = get_goea_nts_prt(goea_results) # List of all fields, printable or not, in namedtuple (nt): log.write("\nnamedtuple FIELDS: {F}\n".format(F=" ".join(goea_nts[0]._fields))) # Print to Excel Spreadsheet title = "Print subset of namedtuple fields" wr_xlsx("nbt3102_subset_nt.xlsx", goea_nts, title=title, **wr_params) # Print to tab-separated file wr_tsv(tsv_nts, goea_nts, **wr_params)
def _wr_3fmt_wrtbl(tsv_nts, goea_results, wr_params, log): """Using functions in the wr_tbl pkg, demonstrate printing a subset of namedtuple fields.""" goea_nts = get_goea_nts_prt(goea_results) # List of all fields, printable or not, in namedtuple (nt): log.write( "\nnamedtuple FIELDS: {F}\n".format(F=" ".join(goea_nts[0]._fields))) # Print to Excel Spreadsheet title = "Print subset of namedtuple fields" wr_xlsx("nbt3102_subset_nt.xlsx", goea_nts, title=title, **wr_params) # Print to tab-separated file wr_tsv(tsv_nts, goea_nts, **wr_params)
def wr_xlsx(self, fout_xlsx, results_nt, **kws): """Write a xlsx file.""" prt_flds = kws[ 'prt_flds'] if 'prt_flds' in kws else self.get_prtflds_default( results_nt) xlsx_data = self._get_nts(results_nt, prt_flds, True, **kws) if 'fld2col_widths' not in kws: kws['fld2col_widths'] = { f: self.default_fld2col_widths.get(f, 8) for f in prt_flds } RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)
def wr_xlsx(self, fout_xlsx): """Write counts of GO terms at all levels and depths.""" from goatools.wr_tbl import wr_xlsx kws = { 'title': "GO Counts in {VER}".format(VER=self.obo.version), 'hdrs': [ "Dep/Lev", "BP Depth", "MF Depth", "CC Depth", "BP Level", "MF Level", "CC Level" ] } wr_xlsx(fout_xlsx, self.get_data(), **kws)
def wr_xlsx(self, fout_xlsx, goea_results, **kws): """Write a xlsx file.""" prt_flds = kws[ 'prt_flds'] if 'prt_flds' in kws else self.get_prtflds_default( goea_results) xlsx_data = get_goea_nts_prt(goea_results, prt_flds, **kws) if 'fld2col_widths' not in kws: kws['fld2col_widths'] = { f: self.default_fld2col_widths.get(f, 8) for f in prt_flds } RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)
def wr_xlsx_nts(self, fout_xlsx, desc2nts, **kws_usr): """Print grouped and sorted GO IDs.""" kws_xlsx = self._get_xlsx_kws(**kws_usr) self._adjust_prt_flds(kws_xlsx, desc2nts, **kws_usr) # 1-D: data to print is a flat list of namedtuples if 'flat' in desc2nts: nts = desc2nts.get('flat') # sys.stdout.write("FLAT NTS: {FLDS}\n".format(FLDS=" ".join(next(iter(nts))._fields))) wr_xlsx(fout_xlsx, nts, **kws_xlsx) # 2-D: data to print is a list of [(section, nts), ... else: sections_hdrgos = desc2nts.get('sections') wr_xlsx_sections(fout_xlsx, sections_hdrgos, **kws_xlsx)
def wr_xlsx_nts(self, fout_xlsx, desc2nts, **kws_usr): """Print grouped and sorted GO IDs.""" # KWS_XLSX: top_n section_prt section_sortby # Adjust xlsx keyword args kws_xlsx = self._get_xlsx_kws(**kws_usr) # KWS_SHADE: shade_hdrgos hdrgo_prt section_sortby top_n shade_hdrgos = self._get_shade_hdrgos(**kws_usr) self._adjust_prt_flds(kws_xlsx, desc2nts, shade_hdrgos) # 1-D: data to print is a flat list of namedtuples if 'flat' in desc2nts: nts = desc2nts.get('flat') # sys.stdout.write("FLAT NTS: {FLDS}\n".format(FLDS=" ".join(next(iter(nts))._fields))) wr_xlsx(fout_xlsx, nts, **kws_xlsx) # 2-D: data to print is a list of [(section, nts), ... else: sections_hdrgos = desc2nts.get('sections') wr_xlsx_sections(fout_xlsx, sections_hdrgos, **kws_xlsx)
def wr_xlsx(self, fout_xlsx, nts): """Write specified namedtuples into an Excel spreadsheet.""" wr_xlsx(fout_xlsx, nts, prt_flds=self.prt_flds, fld2col_widths=self.fld2col_widths)