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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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from goatools.rpt.nts_xfrm import MgrNts |
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def get_study_items(goea_results): |
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"""Get all study items found in a GOATOOLS GOEA (e.g., geneids).""" |
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return MgrNtGOEAs(goea_results).get_study_items() |
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def get_goea_nts_prt(goea_results, **kws): |
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"""Get namedtuples containing user-specified (or default) data from GOATOOLS GOEA results.""" |
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return MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws) |
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class MgrNtGOEAs(object): |
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"""Manage GOATOOLS GOEA namedtuples.""" |
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def __init__(self, goea_results): |
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self.goea_results = list(goea_results) |
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def get_study_items(self): |
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"""Get all study items (e.g., geneids).""" |
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study_items = set() |
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for rec in self.goea_results: |
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study_items |= rec.study_items |
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return study_items |
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def get_nts_strpval(self, fmt="{:8.2e}"): |
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"""Given GOEA namedtuples, return nts w/P-value in string format.""" |
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objntmgr = MgrNts(self.goea_results) |
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dcts = objntmgr.init_dicts() |
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pval_flds = set(k for k in self._get_fieldnames(next(iter(self.goea_results))) if k[:2] == 'p_') |
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for fld_float in pval_flds: |
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fld_str = "s_" + fld_float[2:] |
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objntmgr.add_f2str(dcts, fld_float, fld_str, fmt) |
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return objntmgr.mknts(dcts) |
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def get_goea_nts_prt(self, fldnames=None, **usr_kws): |
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"""Return list of namedtuples removing fields which are redundant or verbose.""" |
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kws = usr_kws.copy() |
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if 'not_fldnames' not in kws: |
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kws['not_fldnames'] = ['goterm', 'parents', 'children', 'id'] |
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if 'rpt_fmt' not in kws: |
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kws['rpt_fmt'] = True |
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return self.get_goea_nts_all(fldnames, **kws) |
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def get_goea_nts_all(self, fldnames=None, **kws): |
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"""Get namedtuples containing user-specified (or default) data from GOEA results. |
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Reformats data from GOEnrichmentRecord objects into lists of |
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namedtuples so the generic table writers may be used. |
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""" |
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# kws: prt_if indent itemid2name(study_items) |
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data_nts = [] # A list of namedtuples containing GOEA results |
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if not self.goea_results: |
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return data_nts |
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keep_if = kws.get('keep_if', None) |
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rpt_fmt = kws.get('rpt_fmt', False) |
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indent = kws.get('indent', False) |
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# I. FIELD (column) NAMES |
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not_fldnames = kws.get('not_fldnames', None) |
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if fldnames is None: |
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fldnames = self._get_fieldnames(self.goea_results[0]) |
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# Ia. Explicitly exclude specific fields from named tuple |
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if not_fldnames is not None: |
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fldnames = [f for f in fldnames if f not in not_fldnames] |
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nttyp = cx.namedtuple("NtGoeaResults", " ".join(fldnames)) |
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goid_idx = fldnames.index("GO") if 'GO' in fldnames else None |
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# II. Loop through GOEA results stored in a GOEnrichmentRecord object |
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for goerec in self.goea_results: |
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vals = self._get_field_values(goerec, fldnames, rpt_fmt, kws.get('itemid2name', None)) |
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if indent: |
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vals[goid_idx] = "".join([goerec.get_indent_dots(), vals[goid_idx]]) |
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ntobj = nttyp._make(vals) |
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if keep_if is None or keep_if(goerec): |
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data_nts.append(ntobj) |
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return data_nts |
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@staticmethod |
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def _get_field_values(item, fldnames, rpt_fmt=None, itemid2name=None): |
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"""Return fieldnames and values of either a namedtuple or GOEnrichmentRecord.""" |
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if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord |
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return item.get_field_values(fldnames, rpt_fmt, itemid2name) |
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if hasattr(item, "_fields"): # Is a namedtuple |
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return [getattr(item, f) for f in fldnames] |
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@staticmethod |
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def _get_fieldnames(item): |
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"""Return fieldnames of either a namedtuple or GOEnrichmentRecord.""" |
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if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord |
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return item.get_prtflds_all() |
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if hasattr(item, "_fields"): # Is a namedtuple |
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return item._fields |
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# Copyright (C) 2010-2018, H Tang et al., All rights reserved. |
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tanghaibao /
goatools
