def __init__(self, sortobj, pval_fld, ver_list):
self.sortobj = sortobj
self.pval_fld = pval_fld
self.ver_list = ver_list
self.objprt = PrtFmt()
self.flds_all = next(iter(self.sortobj.grprobj.go2nt.values()))._fields
self.flds_cur = self._init_flds_cur()
self.desc2nts = self.sortobj.get_desc2nts(hdrgo_prt=False)
def prt_txt(prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
objprt = PrtFmt()
if prtfmt is None:
flds = ['GO', 'NS', 'p_uncorrected',
'ratio_in_study', 'ratio_in_pop', 'depth', 'name', 'study_items']
prtfmt = objprt.get_prtfmt_str(flds)
prtfmt = objprt.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts
def prt_txt(self, prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
objprt = PrtFmt()
if prtfmt is None:
flds = ['GO', 'NS', 'p_uncorrected', 'ratio_in_study', 'ratio_in_pop', 'depth', 'name', 'study_items']
prtfmt = objprt.get_prtfmt_str(flds)
#### prtfmt = " ".join([objprt.default_fld2fmt[f] for f in flds])
#### prtfmt = ("{GO} {NS} {p_uncorrected:5.2e} {ratio_in_study:>6} {ratio_in_pop:>9} "
#### "{depth:02} {name:40} {study_items}\n")
prtfmt = objprt.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts
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)
class GrpWr(object):
"""Write GO term GOEA information, grouped."""
objprtfmt = PrtFmt()
def __init__(self, sortobj, pval_fld, ver_list):
self.sortobj = sortobj
self.pval_fld = pval_fld
self.ver_list = ver_list
self.flds_all = next(iter(self.sortobj.grprobj.go2nt.values()))._fields
self.flds_cur = self._init_flds_cur()
self.desc2nts = self.sortobj.get_desc2nts(hdrgo_prt=False)
# print("nnnnnnnnnnnnnnnnnnnnnttttttttttttttttt", self.flds_all)
def prt_outfiles_grouped(self, outfiles):
"""Write to outfiles."""
for outfile in outfiles:
if outfile.endswith(".xlsx"):
self.wr_xlsx(outfile)
elif outfile.endswith(".txt"):
self.wr_txt(outfile)
else:
self.wr_tsv(outfile)
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_tsv(self, fout_tsv):
"""Print grouped GOEA results into a tab-separated file."""
with open(fout_tsv, 'w') as prt:
kws_tsv = {
'fld2fmt':
{f: '{:8.2e}'
for f in self.flds_cur if f[:2] == 'p_'},
'prt_flds': self.flds_cur
}
prt_tsv_sections(prt, self.desc2nts['sections'], **kws_tsv)
print(" WROTE: {TSV}".format(TSV=fout_tsv))
def wr_txt(self, fout_txt):
"""Write to a file GOEA results in an ASCII text format."""
with open(fout_txt, 'w') as prt:
for line in self.ver_list:
prt.write("{LINE}\n".format(LINE=line))
self.prt_txt(prt)
print(" WROTE: {TXT}".format(TXT=fout_txt))
def prt_tsv(self, prt=sys.stdout):
"""Print an ASCII text format."""
prtfmt = self.objprtfmt.get_prtfmt_str(self.flds_cur)
prt.write("{FLDS}\n".format(FLDS=" ".join(self.flds_cur)))
WrSectionsTxt.prt_sections(prt,
self.desc2nts['sections'],
prtfmt,
secspc=True)
def prt_txt(self, prt=sys.stdout):
"""Print an ASCII text format."""
prtfmt = self.objprtfmt.get_prtfmt_str(self.flds_cur)
prt.write("{FLDS}\n".format(FLDS=" ".join(self.flds_cur)))
WrSectionsTxt.prt_sections(prt,
self.desc2nts['sections'],
prtfmt,
secspc=True)
def _init_flds_cur(self):
"""Choose fields to print from a multitude of available fields."""
flds = []
# ('GO', 'NS', 'enrichment', 'name', 'ratio_in_study', 'ratio_in_pop', 'depth',
# 'p_uncorrected', 'p_bonferroni', 'p_sidak', 'p_holm', 'p_fdr_bh',
# 'pop_n', 'pop_count', 'pop_items'
# 'study_n', 'study_count', 'study_items',
# 'is_ratio_different', 'level', 'is_obsolete',
# 'namespace', 'reldepth', 'alt_ids', 'format_txt', 'hdr_idx',
# 'is_hdrgo', 'is_usrgo', 'num_usrgos', 'hdr1usr01', 'alt', 'GO_name',
# 'dcnt', 'D1', 'tcnt', 'tfreq', 'tinfo', 'childcnt', 'REL',
# 'REL_short', 'rel', 'id')
flds0 = [
'GO', 'NS', 'enrichment', self.pval_fld, 'dcnt', 'tinfo', 'depth',
'ratio_in_study', 'ratio_in_pop', 'name'
]
flds_p = [
f for f in self.flds_all if f[:2] == 'p_' and f != self.pval_fld
]
flds.extend(flds0)
if flds_p:
flds.extend(flds_p)
flds.append('study_count')
flds.append('study_items')
return flds
def __init__(self, sortname, sortobj, ver_list=None):
self.ver_list = ver_list
self.sortname = sortname
self.sortobj = sortobj
self.oprtfmt = PrtFmt()