コード例 #1
0
ファイル: wr_subobo.py プロジェクト: yangfuquan1993/goatools
class WrSubObo(object):
    """Read a large GO-DAG from an obo file. Write a subset GO-DAG into a small obo file."""
    def __init__(self, fin_obo):
        self.fin_obo = fin_obo
        self.godag = GODag(fin_obo)

    def wrobo(self, fout_obo, goid_sources):
        """Write a subset obo file containing GO ID sources and their parents."""
        goids_all = self._get_all_parents(goid_sources).union(goid_sources)
        b_trm = False
        b_prt = True
        with open(fout_obo, 'w') as prt:
            self._prt_info(prt, goid_sources, goids_all)
            with open(self.fin_obo) as ifstrm:
                for line in ifstrm:
                    if not b_trm:
                        if line[:6] == "[Term]":
                            b_trm = True
                            b_prt = False
                    else:
                        if line[:6] == 'id: GO':
                            b_trm = False
                            b_prt = line[4:14] in goids_all
                            if b_prt:
                                prt.write("[Term]\n")
                    if b_prt:
                        prt.write(line)
            sys.stdout.write("  WROTE {N} GO TERMS: {OBO}\n".format(
                N=len(goids_all), OBO=fout_obo))

    def _prt_info(self, prt, goid_sources, goids_all):
        """Print information describing how this obo setset was created."""
        prt.write(
            "Contains {N} GO IDs. Created using {M} GO sources:\n".format(
                N=len(goids_all), M=len(goid_sources)))
        for goid in goid_sources:
            prt.write("    {GO}\n".format(GO=str(self.godag.get(goid, ""))))
        prt.write("\n")

    def _get_all_parents(self, goid_sources):
        """Get all GO ID parents for all GO IG sources."""
        parents = set()
        for goid in goid_sources:
            goterm = self.godag.get(goid, None)
            if goterm is not None:
                parents |= goterm.get_all_parents()
        return parents
コード例 #2
0
class WrSubObo(object):
    """Read a large GO-DAG from an obo file. Write a subset GO-DAG into a small obo file."""
    def __init__(self, fin_obo, optional_attrs=None, load_obsolete=None):
        self.fin_obo = fin_obo
        self.godag = GODag(fin_obo, optional_attrs, load_obsolete)
        self.relationships = optional_attrs is not None and 'relationship' in optional_attrs

    def wrobo(self, fout_obo, goid_sources):
        """Write a subset obo file containing GO ID sources and their parents."""
        goids_all = self._get_goids_all(goid_sources)
        b_trm = False
        b_prt = True
        with open(fout_obo, 'w') as prt:
            self._prt_info(prt, goid_sources, goids_all)
            with open(self.fin_obo) as ifstrm:
                for line in ifstrm:
                    if not b_trm:
                        if line[:6] == "[Term]":
                            b_trm = True
                            b_prt = False
                        elif line[:6] == "[Typedef]":
                            b_prt = True
                    else:
                        if line[:6] == 'id: GO':
                            b_trm = False
                            b_prt = line[4:14] in goids_all
                            if b_prt:
                                prt.write("[Term]\n")
                    if b_prt:
                        prt.write(line)
            sys.stdout.write("  WROTE {N} GO TERMS: {OBO}\n".format(
                N=len(goids_all), OBO=fout_obo))

    def _get_goids_all(self, go_sources):
        """Given GO ID sources and optionally the relationship attribute, return all GO IDs."""
        go2obj_user = {}
        objrel = CurNHigher(self.relationships, self.godag)
        objrel.get_go2obj_cur_n_high(go2obj_user, go_sources)
        goids = set(go2obj_user)
        for goterm in go2obj_user.values():
            if goterm.alt_ids:
                goids.update(goterm.alt_ids)
        return goids

    def _prt_info(self, prt, goid_sources, goids_all):
        """Print information describing how this obo setset was created."""
        prt.write(
            "! Contains {N} GO IDs. Created using {M} GO sources:\n".format(
                N=len(goids_all), M=len(goid_sources)))
        for goid in goid_sources:
            prt.write("!    {GO}\n".format(GO=str(self.godag.get(goid, ""))))
        prt.write("\n")
コード例 #3
0
ファイル: wr_subobo.py プロジェクト: yaoxingqi/goatools
class WrSubObo(object):
    """Read a large GO-DAG from an obo file. Write a subset GO-DAG into a small obo file."""
    def __init__(self, fin_obo=None, optional_attrs=None, load_obsolete=None):
        self.fin_obo = fin_obo
        self.godag = GODag(fin_obo, optional_attrs,
                           load_obsolete) if fin_obo is not None else None
        self.relationships = optional_attrs is not None and 'relationship' in optional_attrs

    def wrobo(self, fout_obo, goid_sources):
        """Write a subset obo file containing GO ID sources and their parents."""
        goids_all = self._get_goids_all(goid_sources)
        with open(fout_obo, 'w') as prt:
            self._prt_info(prt, goid_sources, goids_all)
            self.prt_goterms(prt, self.fin_obo, goids_all)
            print("  WROTE {N} GO TERMS: {OBO}\n".format(N=len(goids_all),
                                                         OBO=fout_obo))

    @staticmethod
    def prt_goterms(fin_obo, goids, prt, b_prt=True):
        """Print the specified GO terms for GO IDs in arg."""
        b_trm = False
        with open(fin_obo) as ifstrm:
            for line in ifstrm:
                if not b_trm:
                    if line[:6] == "[Term]":
                        b_trm = True
                        b_prt = False
                    elif line[:6] == "[Typedef]":
                        b_prt = True
                else:
                    if line[:6] == 'id: GO':
                        b_trm = False
                        b_prt = line[4:14] in goids
                        if b_prt:
                            prt.write("[Term]\n")
                if b_prt:
                    prt.write(line)

    @staticmethod
    def get_goids(fin_obo, name):
        """Get GO IDs whose name matches given name."""
        goids = set()
        # pylint: disable=unsubscriptable-object
        goterm = None
        with open(fin_obo) as ifstrm:
            for line in ifstrm:
                if goterm is not None:
                    semi = line.find(':')
                    if semi != -1:
                        goterm[line[:semi]] = line[semi + 2:].rstrip()
                    else:
                        if name in goterm['name']:
                            goids.add(goterm['id'])
                        goterm = None
                elif line[:6] == "[Term]":
                    goterm = {}
        return goids

    def _get_goids_all(self, go_sources):
        """Given GO ID sources and optionally the relationship attribute, return all GO IDs."""
        go2obj_user = {}
        objrel = CurNHigher(self.relationships, self.godag)
        objrel.get_go2obj_cur_n_high(go2obj_user, go_sources)
        goids = set(go2obj_user)
        for goterm in go2obj_user.values():
            if goterm.alt_ids:
                goids.update(goterm.alt_ids)
        return goids

    def _prt_info(self, prt, goid_sources, goids_all):
        """Print information describing how this obo setset was created."""
        prt.write(
            "! Contains {N} GO IDs. Created using {M} GO sources:\n".format(
                N=len(goids_all), M=len(goid_sources)))
        for goid in goid_sources:
            prt.write("!    {GO}\n".format(GO=str(self.godag.get(goid, ""))))
        prt.write("\n")
コード例 #4
0
from goatools.obo_parser import GODag

obodag = GODag("go-basic.obo")

for i,line in enumerate(open('new_annotations.csv')):
    if i > 0:
        la = line.split("\t")
        gos = la[1].split(',')
        print(la[0])
        outline = []
        for go in gos:
            if go.startswith("GO:"):
                outline.append("{} ({})".format(
                    obodag.get(go).name,
                    go))
        print(",".join(outline))
コード例 #5
0
ファイル: wr_subobo.py プロジェクト: tanghaibao/goatools
class WrSubObo(object):
    """Read a large GO-DAG from an obo file. Write a subset GO-DAG into a small obo file."""

    def __init__(self, fin_obo=None, optional_attrs=None, load_obsolete=None):
        self.fin_obo = fin_obo
        self.godag = GODag(fin_obo, optional_attrs, load_obsolete) if fin_obo is not None else None
        self.relationships = optional_attrs is not None and 'relationship' in optional_attrs

    def wrobo(self, fout_obo, goid_sources):
        """Write a subset obo file containing GO ID sources and their parents."""
        goids_all = self._get_goids_all(goid_sources)
        with open(fout_obo, 'w') as prt:
            self._prt_info(prt, goid_sources, goids_all)
            self.prt_goterms(prt, self.fin_obo, goids_all)
            print("  WROTE {N} GO TERMS: {OBO}\n".format(N=len(goids_all), OBO=fout_obo))

    @staticmethod
    def prt_goterms(fin_obo, goids, prt, b_prt=True):
        """Print the specified GO terms for GO IDs in arg."""
        b_trm = False
        with open(fin_obo) as ifstrm:
            for line in ifstrm:
                if not b_trm:
                    if line[:6] == "[Term]":
                        b_trm = True
                        b_prt = False
                    elif line[:6] == "[Typedef]":
                        b_prt = True
                else:
                    if line[:6] == 'id: GO':
                        b_trm = False
                        b_prt = line[4:14] in goids
                        if b_prt:
                            prt.write("[Term]\n")
                if b_prt:
                    prt.write(line)

    @staticmethod
    def get_goids(fin_obo, name):
        """Get GO IDs whose name matches given name."""
        goids = set()
        # pylint: disable=unsubscriptable-object
        goterm = None
        with open(fin_obo) as ifstrm:
            for line in ifstrm:
                if goterm is not None:
                    semi = line.find(':')
                    if semi != -1:
                        goterm[line[:semi]] = line[semi+2:].rstrip()
                    else:
                        if name in goterm['name']:
                            goids.add(goterm['id'])
                        goterm = None
                elif line[:6] == "[Term]":
                    goterm = {}
        return goids

    def _get_goids_all(self, go_sources):
        """Given GO ID sources and optionally the relationship attribute, return all GO IDs."""
        go2obj_user = {}
        objrel = CurNHigher(self.relationships, self.godag)
        objrel.get_id2obj_cur_n_high(go2obj_user, go_sources)
        goids = set(go2obj_user)
        for goterm in go2obj_user.values():
            if goterm.alt_ids:
                goids.update(goterm.alt_ids)
        return goids

    def _prt_info(self, prt, goid_sources, goids_all):
        """Print information describing how this obo setset was created."""
        prt.write("! Contains {N} GO IDs. Created using {M} GO sources:\n".format(
            N=len(goids_all), M=len(goid_sources)))
        for goid in goid_sources:
            prt.write("!    {GO}\n".format(GO=str(self.godag.get(goid, ""))))
        prt.write("\n")