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"""Manage GOATOOLS GOEA namedtuples.""" |
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__copyright__ = "Copyright (C) 2010-2018, H Tang et al., All rights reserved." |
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__author__ = "DV Klopfenstein" |
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import collections as cx |
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class MgrNts(object): |
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"""Manage GOATOOLS GOEA namedtuples.""" |
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def __init__(self, nts): |
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self.nts = list(nts) |
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def get_set(self, fieldname): |
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"""Get all study items (e.g., geneids).""" |
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set_items = set() |
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for ntdata in self.nts: |
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set_items |= getattr(ntdata, fieldname) |
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return set_items |
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def mknts(self, add_dct): |
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"""Add information from add_dct to a new copy of namedtuples stored in nts.""" |
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nts = [] |
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assert len(add_dct) == len(self.nts) |
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flds = vars(next(iter(self.nts))).keys() + next(iter(add_dct)).keys() |
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ntobj = cx.namedtuple("ntgoea", " ".join(flds)) |
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for dct_new, ntgoea in zip(add_dct, self.nts): |
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dct_curr = ntgoea._asdict() |
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for key, val in dct_new.items(): |
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dct_curr[key] = val |
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nts.append(ntobj(**dct_curr)) |
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return nts |
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def add_f2str(self, dcts, srcfld, dstfld, dstfmt): |
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"""Add a namedtuple field of type string generated from an existing namedtuple field.""" |
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# Example: f2str = objntmgr.add_f2str(dcts, "p_fdr_bh", "s_fdr_bh", "{:8.2e}") |
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# ntobj = self.get_ntobj() |
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# print(ntobj) |
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assert len(dcts) == len(self.nts) |
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for dct, ntgoea in zip(dcts, self.nts): |
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valorig = getattr(ntgoea, srcfld) |
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valstr = dstfmt.format(valorig) |
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dct[dstfld] = valstr |
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def get_ntobj(self): |
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"""Create namedtuple object with GOEA fields.""" |
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if self.nts: |
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return cx.namedtuple("ntgoea", " ".join(vars(next(iter(self.nts))).keys())) |
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def init_dicts(self): |
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"""Return a list of empty dicts to be filled with new data for revised namedtuples.""" |
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return [{} for _ in self.nts] |
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# Copyright (C) 2010-2018, H Tang et al., All rights reserved. |
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tanghaibao /
goatools
