def prt_gos_grouped(self, prt, **kws_grp):
"""Print grouped GO list."""
prtfmt = self.datobj.kws['fmtgo']
wrobj = WrXlsxSortedGos(self.name, self.sortobj)
# Keyword arguments: control content: hdrgo_prt section_prt top_n use_sections
desc2nts = self.sortobj.get_desc2nts(**kws_grp)
wrobj.prt_txt_desc2nts(prt, desc2nts, prtfmt)
def prt_gos_grouped(self, prt, **kws_grp):
"""Print grouped GO list."""
prtfmt = self.datobj.kws['fmtgo']
wrobj = WrXlsxSortedGos(self.name, self.sortobj)
# Keyword arguments: control content: hdrgo_prt section_prt top_n use_sections
desc2nts = self.sortobj.get_desc2nts(**kws_grp)
wrobj.prt_txt_desc2nts(prt, desc2nts, prtfmt)
def cli(self, prt=sys.stdout):
"""Command-line interface for go_draw script."""
kws = self.objdoc.get_docargs(prt=None)
godag = get_godag(kws['obo'], prt=None, loading_bar=False, optional_attrs=['relationship'])
usrgos = GetGOs(godag, max_gos=200).get_usrgos(kws.get('GO_FILE'), prt)
tcntobj = self._get_tcntobj(usrgos, godag, **kws) # Gets TermCounts or None
self.gosubdag = GoSubDag(usrgos, godag, relationships=True, tcntobj=tcntobj, prt=None)
grprdflt = GrouperDflts(self.gosubdag, kws['slims'])
ver_list = [godag.version, grprdflt.ver_goslims]
prt.write("{VER}\n".format(VER="\n".join(ver_list)))
sections = self._read_sections(kws['ifile'])
# print("SECSECSEC", sections)
hdrobj = HdrgosSections(self.gosubdag, grprdflt.hdrgos_dflt, sections)
grprobj = Grouper("init", usrgos, hdrobj, self.gosubdag)
# Write sections
objsecwr = WrSectionsTxt(grprobj, ver_list)
if not os.path.exists(kws['ifile']):
objsecwr.wr_txt_section_hdrgos(kws['ifile'])
objsecwr.wr_txt_section_hdrgos(kws['ofile'])
objsecpy = WrSectionsPy(grprobj, ver_list)
if 'py' in kws:
objsecpy.wr_py_sections(kws['py'], sections, doc=godag.version)
# Write user GO IDs in sections
sortobj = Sorter(grprobj)
objgowr = WrXlsxSortedGos("init", sortobj, ver_list)
objgowr.wr_txt_gos(kws['txt'], sortby=objsecpy.fncsortnt)
#objwr.wr_txt_section_hdrgos(kws['ofile'], sortby=objwr.fncsortnt)
self._prt_cnt_usrgos(usrgos, sys.stdout)
def write(self, fout_xlsx=None, fout_txt=None, verbose=False):
"""Command-line interface for go_draw script."""
sortby = self._get_fncsortnt(self.objgrpd.grprobj.gosubdag.prt_attr['flds'])
kws_sort = {'sortby' if verbose else 'section_sortby': sortby}
sortobj = Sorter(self.objgrpd.grprobj, **kws_sort)
# KWS: hdrgo_prt=True section_prt=None top_n=None use_sections=True
# RET: {sortobj, sections, hdrgo_prt} or {sortobj flat hdrgo_prt}
desc2nts = sortobj.get_desc2nts_fnc(
hdrgo_prt=verbose,
section_prt=True,
top_n=None,
use_sections=True)
# print('FFFF', desc2nts['flds'])
# Write user GO IDs in sections
objgowr = WrXlsxSortedGos("init", sortobj, self.objgrpd.ver_list)
if fout_xlsx is not None:
kws_xlsx = {'shade_hdrgos':verbose}
if not verbose:
kws_xlsx['prt_flds'] = [f for f in desc2nts['flds'] if f not in self.excl_flds]
objgowr.wr_xlsx_nts(fout_xlsx, desc2nts, **kws_xlsx)
fout_desc = '{BASE}_desc.txt'.format(BASE=os.path.splitext(fout_xlsx)[0])
self._wr_ver_n_key(fout_desc, verbose)
if fout_txt is not None:
self._wr_txt_nts(fout_txt, desc2nts, objgowr, verbose)
if fout_xlsx is None and fout_txt is None:
self._prt_ver_n_key(sys.stdout, verbose)
prtfmt = self._get_prtfmt(objgowr, verbose)
summary_dct = objgowr.prt_txt_desc2nts(sys.stdout, desc2nts, prtfmt)
self._prt_ver_n_key(sys.stdout, verbose)
if summary_dct:
print("\n{N} GO IDs in {S} sections".format(
N=desc2nts['num_items'], S=desc2nts['num_sections']))
def write(self, fout_xlsx=None, fout_txt=None, verbose=False):
"""Command-line interface for go_draw script."""
sortby = self._get_fncsortnt(self.objgrpd.grprobj.gosubdag.prt_attr['flds'])
kws_sort = {'sortby' if verbose else 'section_sortby': sortby}
sortobj = Sorter(self.objgrpd.grprobj, **kws_sort)
# KWS: hdrgo_prt=True section_prt=None top_n=None use_sections=True
# RET: {sortobj, sections, hdrgo_prt} or {sortobj flat hdrgo_prt}
desc2nts = sortobj.get_desc2nts_fnc(
hdrgo_prt=verbose,
section_prt=True,
top_n=None,
use_sections=True)
# print('FFFF', desc2nts['flds'])
# Write user GO IDs in sections
objgowr = WrXlsxSortedGos("init", sortobj, self.objgrpd.ver_list)
if fout_xlsx is not None:
kws_xlsx = {'shade_hdrgos':verbose}
if not verbose:
kws_xlsx['prt_flds'] = [f for f in desc2nts['flds'] if f not in self.excl_flds]
objgowr.wr_xlsx_nts(fout_xlsx, desc2nts, **kws_xlsx)
fout_desc = '{BASE}_desc.txt'.format(BASE=os.path.splitext(fout_xlsx)[0])
self._wr_ver_n_key(fout_desc, verbose)
if fout_txt is not None:
self._wr_txt_nts(fout_txt, desc2nts, objgowr, verbose)
if fout_xlsx is None and fout_txt is None:
self._prt_ver_n_key(sys.stdout, verbose)
prtfmt = self._get_prtfmt(objgowr, verbose)
summary_dct = objgowr.prt_txt_desc2nts(sys.stdout, desc2nts, prtfmt)
self._prt_ver_n_key(sys.stdout, verbose)
if summary_dct:
print("\n{N} GO IDs in {S} sections".format(
N=desc2nts['num_items'], S=desc2nts['num_sections']))
def _wr_xlsx(name, grprobj, **kws):
"""Group, sort, and print xlsx file."""
# Exclude ungrouped "Misc." section of sections var(sec_rd)
fout_xlsx = "{NAME}.xlsx".format(NAME=name)
# kws Sorter: hdrgo_prt section_prt top_n use_sections
sortobj = Sorter(grprobj)
desc2nts = sortobj.get_desc2nts(**kws)
objwr = WrXlsxSortedGos(name, sortobj)
# kws WrXlsxSortedGos wr_xlsx_nts: title hdrs
objwr.wr_xlsx_nts(fout_xlsx, desc2nts, **kws)
def _wr_xlsx(name, grprobj, **kws):
"""Group, sort, and print xlsx file."""
# print('\nTEST {} kws_sortobj: {}'.format(name, kws))
# KWS SORT OBJ
kws_sort = {'sortby', 'hdrgo_sortby', 'section_sortby'}
# KWS SORT FUNC: hdrgo_prt section_prt top_n use_sections prtfmt
# Exclude ungrouped "Misc." section of sections var(sec_rd)
fout_xlsx = "{NAME}.xlsx".format(NAME=name)
# kws Sorter: hdrgo_prt section_prt top_n use_sections
sortobj = Sorter(grprobj, **{k:v for k, v in kws.items() if k in kws_sort})
desc2nts = sortobj.get_desc2nts(**kws)
objwr = WrXlsxSortedGos(name, sortobj)
# kws WrXlsxSortedGos wr_xlsx_nts: title hdrs
objwr.wr_xlsx_nts(fout_xlsx, desc2nts, **kws)
def wr_xlsx(self, fout_xlsx):
"""Print grouped GOEA results into an xlsx file."""
objwr = WrXlsxSortedGos("GOEA", self.sortobj)
#### fld2fmt['ratio_in_study'] = '{:>8}'
#### fld2fmt['ratio_in_pop'] = '{:>12}'
#### ntfld2wbfmtdict = {
# ntfld_wbfmt = {
# 'ratio_in_study': {'align':'right'},
# 'ratio_in_pop':{'align':'right'}}
kws_xlsx = {
'title': self.ver_list,
'fld2fmt': {f:'{:8.2e}' for f in self.flds_cur if f[:2] == 'p_'},
#'ntfld_wbfmt': ntfld_wbfmt,
#### 'ntval2wbfmtdict': ntval2wbfmtdict,
#'hdrs': [],
'prt_flds': self.flds_cur}
objwr.wr_xlsx_nts(fout_xlsx, self.desc2nts, **kws_xlsx)
def wr_xlsx(self, fout_xlsx):
"""Print grouped GOEA results into an xlsx file."""
objwr = WrXlsxSortedGos("GOEA", self.sortobj)
#### fld2fmt['ratio_in_study'] = '{:>8}'
#### fld2fmt['ratio_in_pop'] = '{:>12}'
#### ntfld2wbfmtdict = {
# ntfld_wbfmt = {
# 'ratio_in_study': {'align':'right'},
# 'ratio_in_pop':{'align':'right'}}
kws_xlsx = {
'title': self.ver_list,
'fld2fmt': {f:'{:8.2e}' for f in self.flds_cur if f[:2] == 'p_'},
#'ntfld_wbfmt': ntfld_wbfmt,
#### 'ntval2wbfmtdict': ntval2wbfmtdict,
#'hdrs': [],
'prt_flds': self.flds_cur}
objwr.wr_xlsx_nts(fout_xlsx, self.desc2nts, **kws_xlsx)
def wr_xlsx_nts(self, fout_xlsx, desc2nts, **kws):
"""Write grouped and sorted user GO IDs into an xlsx file."""
# kws (content): hdrgo_prt section_prt use_sections
# kws (prt fmt): title fld2col_widths ...
xlsxobj = WrXlsxSortedGos("sortname", self)
xlsxobj.wr_xlsx_nts(fout_xlsx, desc2nts, **kws)