def _init_fld2col_widths():
"""Return default column widths for writing an Excel Spreadsheet."""
# GO info namedtuple fields: NS dcnt level depth GO D1 name
# GO header namedtuple fields: format_txt hdr_idx
fld2col_widths = GoSubDagWr.fld2col_widths.copy()
for fld, wid in GOEnrichmentStudy.default_fld2col_widths.items():
fld2col_widths[fld] = wid
for fld in get_hdridx_flds():
fld2col_widths[fld] = 2
return fld2col_widths
def _init_fld2col_widths(self):
"""Return default column widths for writing an Excel Spreadsheet."""
# GO info namedtuple fields: NS dcnt level depth GO D1 name
# GO header namedtuple fields: format_txt hdr_idx
fld2col_widths = GoSubDagWr.fld2col_widths.copy()
for fld, wid in self.oprtfmt.default_fld2col_widths.items():
fld2col_widths[fld] = wid
for fld in get_hdridx_flds():
fld2col_widths[fld] = 2
return fld2col_widths
def get_go2nt(self, usr_go2nt):
"""Combine user namedtuple fields, GO object fields, and format_txt."""
gos_all = self.get_gos_all()
# Minimum set of namedtuple fields available for use with Sorter on grouped GO IDs
prt_flds_all = get_hdridx_flds() + self.gosubdag.prt_attr['flds']
if not usr_go2nt:
return self.__init_go2nt_dflt(gos_all, prt_flds_all)
usr_nt_flds = next(iter(usr_go2nt.values()))._fields
# If user namedtuple already contains all fields available, then return usr_go2nt
if not set(prt_flds_all).difference(usr_nt_flds):
return self._init_go2nt_aug(usr_go2nt)
# Otherwise, combine user fields and default Sorter fields
return self.__init_go2nt_w_usr(gos_all, usr_go2nt, prt_flds_all)
class NtMaker:
"""Make namedtuples for GO IDs in grouper."""
ntobj = cx.namedtuple("NtHdrIdx", " ".join(get_hdridx_flds()))
def __init__(self, obj):
self.grpname = obj.grpname
self.usrgos = obj.usrgos
self.hdrgos = obj.hdrobj.hdrgos
## assert "GO:0008150" in self.hdrgos
self.go2obj = obj.gosubdag.go2obj
self.hdrgo2usrgos = obj.hdrgo2usrgos
self.hdrgo_is_usrgo = obj.hdrgo_is_usrgo
def get_nt(self, goid_user):
"""Get Grouper namedtuple for user GO ID."""
goid_main = self.go2obj[goid_user].id
goid_in_hdrgos = goid_main in self.hdrgo2usrgos
goid_in_usrgos = goid_user in self.hdrgo_is_usrgo
# format_txt = int(goid_in_hdrgos or goobj.id in self.hdrgos)
format_txt = int(goid_in_hdrgos)
# namedtuple grouping fields
hdr1usr01 = self._get_hdr1usr01(goid_in_hdrgos, goid_in_usrgos)
return self.ntobj(format_txt=format_txt,
hdr_idx=format_txt,
is_hdrgo=goid_in_hdrgos,
is_usrgo=goid_in_usrgos,
num_usrgos=self._get_num_usrgos(
goid_user, goid_in_hdrgos, goid_in_usrgos),
hdr1usr01=hdr1usr01)
def _get_num_usrgos(self, goid_main, goid_in_hdrgos, goid_in_usrgos):
"""Get the number of user GO IDs under a header GO ID."""
if not goid_in_hdrgos:
return "."
num_goids = len(self.hdrgo2usrgos[goid_main]) + int(goid_in_usrgos)
assert num_goids != 0, "{NAME} MAIN({GO}) num_goids({N})\n{HDRUSR}".format(
NAME=self.grpname,
GO=goid_main,
N=num_goids,
HDRUSR="******".join(sorted(self.hdrgos)))
return num_goids
@staticmethod
def _get_hdr1usr01(goid_in_hdrgos, goid_in_usrgos):
"""Get string indicating if GO is also a header GO."""
if goid_in_hdrgos:
return "**" if goid_in_usrgos else "*"
return ""