MgrNtGOEAs

Complexity

Total Complexity

24

Size/Duplication

Total Lines	69
Duplicated Lines	0 %

Importance

Changes	1
Bugs	0	Features	0

6 Methods

Rating	Name	Duplication	Size	Complexity
A	_get_field_values()	0	7	4
A	get_goea_nts_prt()	0	8	3
F	get_goea_nts_all()	0	31	11
A	__init__()	0	2	1
A	get_study_items()	0	6	2
A	_get_fieldnames()	0	7	3

"""Manage GOATOOLS GOEA namedtuples."""

__copyright__ = "Copyright (C) 2010-2018, H Tang et al., All rights reserved."
__author__ = "DV Klopfenstein"

import collections as cx


def get_study_items(goea_results):
    """Get all study items found in a GOATOOLS GOEA (e.g., geneids)."""
    return MgrNtGOEAs(goea_results).get_study_items()

def get_goea_nts_prt(goea_results, **kws):
    """Get namedtuples containing user-specified (or default) data from GOATOOLS GOEA results."""
    return MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)


class MgrNtGOEAs(object):
    """Manage GOATOOLS GOEA namedtuples."""

    def __init__(self, goea_results):
        self.goea_results = goea_results

    def get_study_items(self):
        """Get all study items (e.g., geneids)."""
        study_items = set()
        for rec in self.goea_results:
            study_items |= rec.study_items
        return study_items

    def get_goea_nts_prt(self, fldnames=None, **usr_kws):
        """Return list of namedtuples removing fields which are redundant or verbose."""
        kws = usr_kws.copy()
        if 'not_fldnames' not in kws:
            kws['not_fldnames'] = ['goterm', 'parents', 'children', 'id']
        if 'rpt_fmt' not in kws:
            kws['rpt_fmt'] = True
        return self.get_goea_nts_all(fldnames, **kws)

    def get_goea_nts_all(self, fldnames=None, **kws):
        """Get namedtuples containing user-specified (or default) data from GOEA results.

            Reformats data from GOEnrichmentRecord objects into lists of
            namedtuples so the generic table writers may be used.
        """
        # kws: prt_if indent itemid2name(study_items)
        data_nts = [] # A list of namedtuples containing GOEA results
        if not self.goea_results:
            return data_nts
        keep_if = kws.get('keep_if', None)
        rpt_fmt = kws.get('rpt_fmt', False)
        indent = kws.get('indent', False)
        # I. FIELD (column) NAMES
        not_fldnames = kws.get('not_fldnames', None)
        if fldnames is None:
            fldnames = self._get_fieldnames(self.goea_results[0])
        # Ia. Explicitly exclude specific fields from named tuple
        if not_fldnames is not None:
            fldnames = [f for f in fldnames if f not in not_fldnames]
        nttyp = cx.namedtuple("NtGoeaResults", " ".join(fldnames))
        goid_idx = fldnames.index("GO") if 'GO' in fldnames else None
        # II. Loop through GOEA results stored in a GOEnrichmentRecord object
        for goerec in self.goea_results:
            vals = self._get_field_values(goerec, fldnames, rpt_fmt, kws.get('itemid2name', None))
            if indent:
                vals[goid_idx] = "".join([goerec.get_indent_dots(), vals[goid_idx]])
            ntobj = nttyp._make(vals)
            if keep_if is None or keep_if(goerec):
                data_nts.append(ntobj)
        return data_nts

    @staticmethod
    def _get_field_values(item, fldnames, rpt_fmt=None, itemid2name=None):
        """Return fieldnames and values of either a namedtuple or GOEnrichmentRecord."""
        if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord
            return item.get_field_values(fldnames, rpt_fmt, itemid2name)
        if hasattr(item, "_fields"): # Is a namedtuple
            return [getattr(item, f) for f in fldnames]

    @staticmethod
    def _get_fieldnames(item):
        """Return fieldnames of either a namedtuple or GOEnrichmentRecord."""
        if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord
            return item.get_prtflds_all()
        if hasattr(item, "_fields"): # Is a namedtuple
            return item._fields

# Copyright (C) 2010-2018, H Tang et al., All rights reserved.