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)
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)
