GOEnrichmentStudy._run_multitest_statsmodels() - Code Metrics - Inspection of "Move wr_hier script implmentation out of godag and..." - tanghaibao/goatools - Measure and Improve Code Quality continuously with Scrutinizer

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GOEnrichmentStudy._run_multitest_statsmodels() A

↳ Parent: GOEnrichmentStudy
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#!/usr/bin/env python
# -*- coding: UTF-8 -*-

"""
python %prog study.file population.file gene-association.file

This program returns P-values for functional enrichment in a cluster of
study genes using Fisher's exact test, and corrected for multiple testing
(including Bonferroni, Holm, Sidak, and false discovery rate)
"""

from __future__ import print_function
from __future__ import absolute_import


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

import sys
import collections as cx
import datetime

from goatools.multiple_testing import Methods
from goatools.multiple_testing import Bonferroni
from goatools.multiple_testing import Sidak
from goatools.multiple_testing import HolmBonferroni
from goatools.multiple_testing import FDR
from goatools.multiple_testing import calc_qval
from goatools.ratio import get_terms, count_terms, is_ratio_different
import goatools.wr_tbl as RPT
from goatools.pvalcalc import FisherFactory

from goatools.rpt.goea_nt_xfrm import MgrNtGOEAs

class GOEnrichmentRecord(object):
    """Represents one result (from a single GOTerm) in the GOEnrichmentStudy
    """
    namespace2NS = cx.OrderedDict([
        ('biological_process', 'BP'),
        ('molecular_function', 'MF'),
        ('cellular_component', 'CC')])

    # Fields seen in every enrichment result
    _fldsdefprt = [
        "GO",
        "NS",
        "enrichment",
        "name",
        "ratio_in_study",
        "ratio_in_pop",
        "p_uncorrected",
        "depth",
        "study_count",
        "study_items"]
    _fldsdeffmt = ["%s"]*3 + ["%-30s"] + ["%d/%d"] * 2 + ["%.3g"] + ["%d"] * 2 + ["%15s"]

    _flds = set(_fldsdefprt).intersection(
        set(['study_items', 'study_count', 'study_n', 'pop_items', 'pop_count', 'pop_n']))

    def __init__(self, **kwargs):
        # Methods seen in current enrichment result
        self.method_flds = []
        for key, val in kwargs.items():
            setattr(self, key, val)
            if key == 'ratio_in_study':
                setattr(self, 'study_count', val[0])
                setattr(self, 'study_n', val[1])
            if key == 'ratio_in_pop':
                setattr(self, 'pop_count', val[0])
                setattr(self, 'pop_n', val[1])
        self._init_enrichment()
        self.goterm = None  # the reference to the GOTerm

    def get_method_name(self):
        """Return name of first method in the method_flds list."""
        return self.method_flds[0].fieldname

    def get_pvalue(self):
        """Returns pval for 1st method, if it exists. Else returns uncorrected pval."""
        if self.method_flds:
            return getattr(self, "p_{m}".format(m=self.get_method_name()))
        return getattr(self, "p_uncorrected")

    def set_corrected_pval(self, nt_method, pvalue):
        """Add object attribute based on method name."""
        self.method_flds.append(nt_method)
        fieldname = "".join(["p_", nt_method.fieldname])
        setattr(self, fieldname, pvalue)

    def __str__(self, indent=False):
        field_data = [getattr(self, f, "n.a.") for f in self._fldsdefprt[:-1]] + \
                     [getattr(self, "p_{}".format(m.fieldname)) for m in self.method_flds] + \
                     [", ".join(sorted(getattr(self, self._fldsdefprt[-1], set())))]
        fldsdeffmt = self._fldsdeffmt
        field_formatter = fldsdeffmt[:-1] + ["%.3g"]*len(self.method_flds) + [fldsdeffmt[-1]]
        self._chk_fields(field_data, field_formatter)

        # default formatting only works for non-"n.a" data
        for idx, fld in enumerate(field_data):
            if fld == "n.a.":
                field_formatter[idx] = "%s"

        # print dots to show the level of the term
        dots = self.get_indent_dots() if indent else ""
        prtdata = "\t".join(a % b for (a, b) in zip(field_formatter, field_data))
        return "".join([dots, prtdata])

    def get_indent_dots(self):
        """Get a string of dots ("....") representing the level of the GO term."""
        return "." * self.goterm.level if self.goterm is not None else ""

    @staticmethod
    def _chk_fields(field_data, field_formatter):
        """Check that expected fields are present."""
        if len(field_data) == len(field_formatter):
            return
        len_dat = len(field_data)
        len_fmt = len(field_formatter)
        msg = [
            "FIELD DATA({d}) != FORMATTER({f})".format(d=len_dat, f=len_fmt),
            "DAT({N}): {D}".format(N=len_dat, D=field_data),
            "FMT({N}): {F}".format(N=len_fmt, F=field_formatter)]
        raise Exception("\n".join(msg))

    def __repr__(self):
        return "GOEnrichmentRecord({GO})".format(GO=self.GO)

    def set_goterm(self, go2obj):
        """Set goterm and copy GOTerm's name and namespace."""
        self.goterm = go2obj.get(self.GO, None)
        present = self.goterm is not None
        self.name = self.goterm.name if present else "n.a."
        self.NS = self.namespace2NS[self.goterm.namespace] if present else "XX"

    def _init_enrichment(self):
        """Mark as 'enriched' or 'purified'."""
        self.enrichment = 'e' if ((1.0 * self.study_count / self.study_n) >
                                  (1.0 * self.pop_count / self.pop_n)) else 'p'

    def update_remaining_fldsdefprt(self, min_ratio=None):
        """Finish updating self (GOEnrichmentRecord) field, is_ratio_different."""
        self.is_ratio_different = is_ratio_different(min_ratio, self.study_count,
                                                     self.study_n, self.pop_count, self.pop_n)


    # -------------------------------------------------------------------------------------
    # Methods for getting flat namedtuple values from GOEnrichmentRecord object
    def get_prtflds_default(self):
        """Get default fields."""
        return self._fldsdefprt[:-1] + \
               ["p_{M}".format(M=m.fieldname) for m in self.method_flds] + \
               [self._fldsdefprt[-1]]

    def get_prtflds_all(self):
        """When converting to a namedtuple, get all possible fields in their original order."""
        flds = []
        dont_add = set(['_parents', 'method_flds', 'relationship_rev', 'relationship'])
        # Fields: GO NS enrichment name ratio_in_study ratio_in_pop p_uncorrected
        #         depth study_count p_sm_bonferroni p_fdr_bh study_items
        self._flds_append(flds, self.get_prtflds_default(), dont_add)
        # Fields: GO NS goterm
        #         ratio_in_pop pop_n pop_count pop_items name
        #         ratio_in_study study_n study_count study_items
        #         method_flds enrichment p_uncorrected p_sm_bonferroni p_fdr_bh
        self._flds_append(flds, vars(self).keys(), dont_add)
        # Fields: name level is_obsolete namespace id depth parents children _parents alt_ids
        self._flds_append(flds, vars(self.goterm).keys(), dont_add)
        return flds

    @staticmethod
    def _flds_append(flds, addthese, dont_add):
        """Retain order of fields as we add them once to the list."""
        for fld in addthese:
            if fld not in flds and fld not in dont_add:
                flds.append(fld)

    def get_field_values(self, fldnames, rpt_fmt=True, itemid2name=None):
        """Get flat namedtuple fields for one GOEnrichmentRecord."""
        row = []
        # Loop through each user field desired
        for fld in fldnames:
            # 1. Check the GOEnrichmentRecord's attributes
            val = getattr(self, fld, None)
            if val is not None:
                if rpt_fmt:
                    val = self._get_rpt_fmt(fld, val, itemid2name)
                row.append(val)
            else:
                # 2. Check the GO object for the field
                val = getattr(self.goterm, fld, None)
                if rpt_fmt:
                    val = self._get_rpt_fmt(fld, val, itemid2name)
                if val is not None:
                    row.append(val)
                else:
                    # 3. Field not found, raise Exception
                    self._err_fld(fld, fldnames)
            if rpt_fmt:
                assert not isinstance(val, list), \
                   "UNEXPECTED LIST: FIELD({F}) VALUE({V}) FMT({P})".format(
                       P=rpt_fmt, F=fld, V=val)
        return row

    @staticmethod
    def _get_rpt_fmt(fld, val, itemid2name=None):
        """Return values in a format amenable to printing in a table."""
        if fld.startswith("ratio_"):
            return "{N}/{TOT}".format(N=val[0], TOT=val[1])
        elif fld in set(['study_items', 'pop_items', 'alt_ids']):
            if itemid2name is not None:
                val = [itemid2name.get(v, v) for v in val]
            return ", ".join([str(v) for v in sorted(val)])
        return val

    def _err_fld(self, fld, fldnames):
        """Unrecognized field. Print detailed Failure message."""
        msg = ['ERROR. UNRECOGNIZED FIELD({F})'.format(F=fld)]
        actual_flds = set(self.get_prtflds_default() + self.goterm.__dict__.keys())
        bad_flds = set(fldnames).difference(set(actual_flds))
        if bad_flds:
            msg.append("\nGOEA RESULT FIELDS: {}".format(" ".join(self._fldsdefprt)))
            msg.append("GO FIELDS: {}".format(" ".join(self.goterm.__dict__.keys())))
            msg.append("\nFATAL: {N} UNEXPECTED FIELDS({F})\n".format(
                N=len(bad_flds), F=" ".join(bad_flds)))
            msg.append("  {N} User-provided fields:".format(N=len(fldnames)))
            for idx, fld in enumerate(fldnames, 1):
                mrk = "ERROR -->" if fld in bad_flds else ""
                msg.append("  {M:>9} {I:>2}) {F}".format(M=mrk, I=idx, F=fld))
        raise Exception("\n".join(msg))


class GOEnrichmentStudy(object):
    """Runs Fisher's exact test, as well as multiple corrections
    """
    # Default Excel table column widths for GOEA results
    default_fld2col_widths = {
        'NS'        :  3,
        'GO'        : 12,
        'alt'       :  2,
        'level'     :  3,
        'depth'     :  3,
        'enrichment':  1,
        'name'      : 60,
        'ratio_in_study':  8,
        'ratio_in_pop'  : 12,
        'study_items'   : 15,
    }

    def __init__(self, pop, assoc, obo_dag, propagate_counts=True, alpha=.05, methods=None, **kws):
        self.log = kws['log'] if 'log' in kws else sys.stdout
        self._run_multitest = {
            'local':lambda iargs: self._run_multitest_local(iargs),
            'statsmodels':lambda iargs: self._run_multitest_statsmodels(iargs)}
        self.pop = set(pop)
        self.pop_n = len(pop)
        self.assoc = assoc
        self.obo_dag = obo_dag
        self.alpha = alpha
        if methods is None:
            methods = ["bonferroni", "sidak", "holm"]
        self.methods = Methods(methods)
        self.pval_obj = FisherFactory(**kws).pval_obj

        if propagate_counts:
            sys.stderr.write("Propagating term counts to parents ..\n")
            obo_dag.update_association(assoc)
        self.go2popitems = get_terms("population", pop, assoc, obo_dag, self.log)

    def run_study(self, study, **kws):
        """Run Gene Ontology Enrichment Study (GOEA) on study ids."""
        # Key-word arguments:
        methods = Methods(kws['methods']) if 'methods' in kws else self.methods
        alpha = kws['alpha'] if 'alpha' in kws else self.alpha
        log = kws['log'] if 'log' in kws else self.log
        # Calculate uncorrected pvalues
        results = self.get_pval_uncorr(study, log)
        if not results:
            return []

        if log is not None:
            log.write("  {MSG}\n".format(MSG="\n  ".join(self.get_results_msg(results, study))))

        # Do multipletest corrections on uncorrected pvalues and update results
        self._run_multitest_corr(results, methods, alpha, study, log)

        for rec in results:
            # get go term for name and level
            rec.set_goterm(self.obo_dag)

        # 'keep_if' can be used to keep only significant GO terms. Example:
        #     >>> keep_if = lambda nt: nt.p_fdr_bh < 0.05 # if results are significant
        #     >>> goea_results = goeaobj.run_study(geneids_study, keep_if=keep_if)
        if 'keep_if' in kws:
            keep_if = kws['keep_if']
            results = [r for r in results if keep_if(r)]

        # Default sort order: First, sort by BP, MF, CC. Second, sort by pval
        results.sort(key=lambda r: [r.NS, r.enrichment, r.p_uncorrected])
        return results # list of GOEnrichmentRecord objects

    def run_study_nts(self, study, **kws):
        """Run GOEA on study ids. Return results as a list of namedtuples."""
        goea_results = self.run_study(study, **kws)
        return MgrNtGOEAs(goea_results).get_goea_nts_all()

    def get_results_msg(self, results, study):
        """Return summary for GOEA results."""
        # To convert msg list to string: "\n".join(msg)
        msg = []
        if results:
            fmt = "{M:6,} GO terms are associated with {N:6,} of {NT:6,}"
            stu_items, num_gos_stu = self.get_item_cnt(results, "study_items")
            pop_items, num_gos_pop = self.get_item_cnt(results, "pop_items")
            stu_txt = fmt.format(N=len(stu_items), M=num_gos_stu, NT=len(set(study)))
            pop_txt = fmt.format(N=len(pop_items), M=num_gos_pop, NT=self.pop_n)
            msg.append("{POP} population items".format(POP=pop_txt))
            msg.append("{STU} study items".format(STU=stu_txt))
        return msg

    def get_pval_uncorr(self, study, log=sys.stdout):
        """Calculate the uncorrected pvalues for study items."""
        results = []
        study_in_pop = self.pop.intersection(study)
        # " 99%    378 of    382 study items found in population"
        go2studyitems = get_terms("study", study_in_pop, self.assoc, self.obo_dag, log)
        pop_n, study_n = self.pop_n, len(study_in_pop)
        allterms = set(go2studyitems).union(set(self.go2popitems))
        if log is not None:
            study_n_orig = len(study)
            log.write("{R:3.0f}% {N:>6,} of {M:>6,} study items found in population({P})\n".format(
                N=study_n, M=study_n_orig, P=pop_n, R=100.0*study_n/study_n_orig))
            log.write("Calculating {N:,} uncorrected p-values using {PFNC}\n".format(
                N=len(allterms), PFNC=self.pval_obj.name))
        calc_pvalue = self.pval_obj.calc_pvalue

        for goid in allterms:
            study_items = go2studyitems.get(goid, set())
            study_count = len(study_items)
            pop_items = self.go2popitems.get(goid, set())
            pop_count = len(pop_items)

            one_record = GOEnrichmentRecord(
                GO=goid,
                p_uncorrected=calc_pvalue(study_count, study_n, pop_count, pop_n),
                study_items=study_items,
                pop_items=pop_items,
                ratio_in_study=(study_count, study_n),
                ratio_in_pop=(pop_count, pop_n))

            results.append(one_record)

        return results

    def _run_multitest_corr(self, results, usrmethod_flds, alpha, study, log):
        """Do multiple-test corrections on uncorrected pvalues."""
        assert 0 < alpha < 1, "Test-wise alpha must fall between (0, 1)"
        pvals = [r.p_uncorrected for r in results]
        ntobj = cx.namedtuple("ntobj", "results pvals alpha nt_method study")

        for nt_method in usrmethod_flds:
            ntmt = ntobj(results, pvals, alpha, nt_method, study)
            self._run_multitest[nt_method.source](ntmt)
            if log is not None:
                self._log_multitest_corr(log, results, ntmt, alpha)

    def _log_multitest_corr(self, log, results, ntmt, alpha):
        """Print information regarding multitest correction results."""
        ntm = ntmt.nt_method
        attr_mult = "p_{M}".format(M=self.methods.get_fieldname(ntm.source, ntm.method))
        sig_cnt = sum(1 for r in results if getattr(r, attr_mult) < alpha)
        log.write("{N:8,} GO terms found significant (< {A}=alpha) after ".format(
            N=sig_cnt, A=alpha))
        log.write("multitest correction: ")
        log.write("{MSRC} {METHOD}\n".format(MSRC=ntm.source, METHOD=ntm.method))

    def _run_multitest_statsmodels(self, ntmt):
        """Use multitest mthods that have been implemented in statsmodels."""
        # Only load statsmodels if it is used
        multipletests = self.methods.get_statsmodels_multipletests()
        results = multipletests(ntmt.pvals, ntmt.alpha, ntmt.nt_method.method)
        pvals_corrected = results[1] # reject_lst, pvals_corrected, alphacSidak, alphacBonf
        self._update_pvalcorr(ntmt, pvals_corrected)

    def _run_multitest_local(self, ntmt):
        """Use multitest mthods that have been implemented locally."""
        corrected_pvals = None
        method = ntmt.nt_method.method
        if method == "bonferroni":
            corrected_pvals = Bonferroni(ntmt.pvals, ntmt.alpha).corrected_pvals
        elif method == "sidak":
            corrected_pvals = Sidak(ntmt.pvals, ntmt.alpha).corrected_pvals
        elif method == "holm":
            corrected_pvals = HolmBonferroni(ntmt.pvals, ntmt.alpha).corrected_pvals
        elif method == "fdr":
            # get the empirical p-value distributions for FDR
            term_pop = getattr(self, 'term_pop', None)
            if term_pop is None:
                term_pop = count_terms(self.pop, self.assoc, self.obo_dag)
            p_val_distribution = calc_qval(len(ntmt.study),
                                           self.pop_n,
                                           self.pop, self.assoc,
                                           term_pop, self.obo_dag)
            corrected_pvals = FDR(p_val_distribution,
                                  ntmt.results, ntmt.alpha).corrected_pvals

        self._update_pvalcorr(ntmt, corrected_pvals)

    @staticmethod
    def _update_pvalcorr(ntmt, corrected_pvals):
        """Add data members to store multiple test corrections."""
        if corrected_pvals is None:
            return
        for rec, val in zip(ntmt.results, corrected_pvals):
            rec.set_corrected_pval(ntmt.nt_method, val)

    # Methods for writing results into tables: text, tab-separated, Excel spreadsheets
    def wr_txt(self, fout_txt, goea_results, prtfmt=None, **kws):
        """Print GOEA results to text file."""
        if not goea_results:
            sys.stdout.write("      0 GOEA results. NOT WRITING {FOUT}\n".format(FOUT=fout_txt))
            return
        with open(fout_txt, 'w') as prt:
            if 'title' in kws:
                prt.write("{TITLE}\n".format(TITLE=kws['title']))
            data_nts = self.prt_txt(prt, goea_results, prtfmt, **kws)
            log = self.log if self.log is not None else sys.stdout
            log.write("  {N:>5} GOEA results for {CUR:5} study items. WROTE: {F}\n".format(
                N=len(data_nts),
                CUR=len(MgrNtGOEAs(goea_results).get_study_items()),
                F=fout_txt))

    def prt_txt(self, prt, goea_results, prtfmt=None, **kws):
        """Print GOEA results in text format."""
        if prtfmt is None:
            prtfmt = ("{GO} {NS} {p_uncorrected:5.2e} {ratio_in_study:>6} {ratio_in_pop:>9} "
                      "{depth:02} {name:40} {study_items}\n")
        prtfmt = self.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)
        prt_flds = kws.get('prt_flds', self.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:self.default_fld2col_widths.get(f, 8) for f in prt_flds}
        RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)

    def wr_tsv(self, fout_tsv, goea_results, **kws):
        """Write tab-separated table data to file"""
        prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
        tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
        RPT.wr_tsv(fout_tsv, tsv_data, **kws)

    def prt_tsv(self, prt, goea_results, **kws):
        """Write tab-separated table data"""
        prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
        tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
        RPT.prt_tsv(prt, tsv_data, prt_flds, **kws)

    @staticmethod
    def adjust_prtfmt(prtfmt):
        """Adjust format_strings for legal values."""
        prtfmt = prtfmt.replace("{p_holm-sidak", "{p_holm_sidak")
        prtfmt = prtfmt.replace("{p_simes-hochberg", "{p_simes_hochberg")
        return prtfmt

    @staticmethod
    def get_ns2nts(results, fldnames=None, **kws):
        """Get namedtuples of GOEA results, split into BP, MF, CC."""
        ns2nts = cx.defaultdict(list)
        nts = MgrNtGOEAs(results).get_goea_nts_all(fldnames, **kws)
        for ntgoea in nts:
            ns2nts[ntgoea.NS].append(ntgoea)
        return ns2nts

    @staticmethod
    def get_item_cnt(results, attrname="study_items"):
        """Get all study or population items (e.g., geneids)."""
        items = set()
        go_cnt = 0
        for rec in results:
            if hasattr(rec, attrname):
                items_cur = getattr(rec, attrname)
                # Only count GO term if there are items in the set.
                if len(items_cur) != 0:
                    items |= items_cur
                    go_cnt += 1
        return items, go_cnt

    @staticmethod
    def get_prtflds_default(results):
        """Get default fields names. Used in printing GOEA results.

           Researchers can control which fields they want to print in the GOEA results
           or they can use the default fields.
        """
        if results:
            return results[0].get_prtflds_default()
        return []

    @staticmethod
    def print_summary(results, min_ratio=None, indent=False, pval=0.05):
        """Print summary."""
        import goatools

        # Header contains provenance and parameters
        date = datetime.date.today()
        print("# Generated by GOATOOLS v{0} ({1})".format(goatools.__version__, date))
        print("# min_ratio={0} pval={1}".format(min_ratio, pval))

        # field names for output
        if results:
            print("\t".join(GOEnrichmentStudy.get_prtflds_default(results)))

        for rec in results:
            # calculate some additional statistics
            # (over_under, is_ratio_different)
            rec.update_remaining_fldsdefprt(min_ratio=min_ratio)

            if pval is not None and rec.p_uncorrected >= pval:
                continue

            if rec.is_ratio_different:
                print(rec.__str__(indent=indent))

    def wr_py_goea_results(self, fout_py, goea_results, **kws):
        """Save GOEA results into Python package containing list of namedtuples."""
        var_name = kws.get("var_name", "goea_results")
        docstring = kws.get("docstring", "")
        sortby = kws.get("sortby", None)
        if goea_results:
            from goatools.nt_utils import wr_py_nts
            nts_goea = goea_results
            # If list has GOEnrichmentRecords or verbose namedtuples, exclude some fields.
            if hasattr(goea_results[0], "_fldsdefprt") or hasattr(goea_results[0], 'goterm'):
                # Exclude some attributes from the namedtuple when saving results
                # to a Python file because the information is redundant or verbose.
                nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
            docstring = "\n".join([docstring, "# {VER}\n\n".format(VER=self.obo_dag.version)])
            assert hasattr(nts_goea[0], '_fields')
            if sortby is None:
                sortby = lambda nt: [getattr(nt, 'namespace'), getattr(nt, 'enrichment'),
                                     getattr(nt, 'p_uncorrected'), getattr(nt, 'depth'),
                                     getattr(nt, 'GO')]
            nts_goea = sorted(nts_goea, key=sortby)
            wr_py_nts(fout_py, nts_goea, docstring, var_name)

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

tanghaibao / goatools

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GOEnrichmentStudy._run_multitest_statsmodels() A

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