How to use get_family method in avocado

Best Python code snippet using avocado_python

test_x_dominant.py

Source:test_x_dominant.py

1from genmod.annotate_models.models import check_X_dominant2from genmod.vcf_tools import Genotype3from ped_parser import FamilyParser4FAMILY_FILE = "tests/fixtures/recessive_trio.ped"5def get_family(family_file = None, family_lines = None):6    """Return a family object7    8    """9    family = None10    if family_file:11        family = FamilyParser(open(family_file, 'r'))12    elif family_lines:13        family = FamilyParser(family_lines)14        15    return family16################# Test affected ###############17def test_x_affected_recessive_male():18    """Test a sick male19    """20    family_lines = [21        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",22        "1\tproband\t0\t0\t1\t2\n"23    ]24    25    family = get_family(family_lines=family_lines)26    27    recessive_variant = {'genotypes': {}}28    recessive_variant['genotypes']['proband'] = Genotype(**{'GT':'0/1'})29    30    assert check_X_dominant(31        variant = recessive_variant,32        family = family33    ) == True34def test_x_affected_recessive_female():35    """Test a sick heterozygote female36    37    Females needs to bo hom alt to follow pattern38    """39    family_lines = [40        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",41        "1\tproband\t0\t0\t2\t2\n"42    ]43    44    family = get_family(family_lines=family_lines)45    46    recessive_variant = {'genotypes': {}}47    recessive_variant['genotypes']['proband'] = Genotype(**{'GT':'0/1'})48    49    assert check_X_dominant(50        variant = recessive_variant,51        family = family52    ) == True53def test_x_affected_homozygote_male():54    """Test an affected homozygote male"""55    56    family_lines = [57        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",58        "1\tproband\t0\t0\t1\t2\n"59    ]60    61    family = get_family(family_lines=family_lines)62    63    homozygote_variant = {'genotypes': {}}64    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'1/1'})65    66    assert check_X_dominant(67        variant = homozygote_variant,68        family = family69    ) == True70def test_x_affected_homozygote_female():71    """Test an affected homozygote male"""72    73    family_lines = [74        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",75        "1\tproband\t0\t0\t2\t2\n"76    ]77    78    family = get_family(family_lines=family_lines)79    80    homozygote_variant = {'genotypes': {}}81    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'1/1'})82    83    assert check_X_dominant(84        variant = homozygote_variant,85        family = family86    ) == True87def test_x_affected_male_ref_call():88    """Test an affected ref call male"""89    90    family_lines = [91        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",92        "1\tproband\t0\t0\t1\t2\n"93    ]94    95    family = get_family(family_lines=family_lines)96    97    homozygote_variant = {'genotypes': {}}98    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'0/0'})99    100    assert check_X_dominant(101        variant = homozygote_variant,102        family = family103    ) == False104def test_x_affected_female_ref_call():105    """Test an affected ref call male"""106    107    family_lines = [108        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",109        "1\tproband\t0\t0\t2\t2\n"110    ]111    112    family = get_family(family_lines=family_lines)113    114    homozygote_variant = {'genotypes': {}}115    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'0/0'})116    117    assert check_X_dominant(118        variant = homozygote_variant,119        family = family120    ) == False121    122def test_x_affected_no_call_male():123    """Test a sick male with no gt call124    125    This should be true since there is no information that contradicts the model126    """127    family_lines = [128        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",129        "1\tproband\t0\t0\t1\t2\n"130    ]131    132    family = get_family(family_lines=family_lines)133    134    no_call_variant = {'genotypes': {}}135    no_call_variant['genotypes']['proband'] = Genotype(**{'GT':'./.'})136    137    assert check_X_dominant(138        variant = no_call_variant,139        family = family140    ) == True141def test_x_affected_no_call_male_strict():142    """Test a sick male with no gt call143    144    This should not be true since we allways need 'proof'145    for an inheritance pattern if strict mode.146    """147    family_lines = [148        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",149        "1\tproband\t0\t0\t1\t2\n"150    ]151    152    family = get_family(family_lines=family_lines)153    154    no_call_variant = {'genotypes': {}}155    no_call_variant['genotypes']['proband'] = Genotype(**{'GT':'./.'})156    157    assert check_X_dominant(158        variant = no_call_variant,159        family = family,160        strict = True161    ) == False162############### Test healthy ##############163def test_x_healthy_recessive_male():164    """Test a healthy recessive male165    """166    family_lines = [167        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",168        "1\tproband\t0\t0\t1\t1\n"169    ]170    171    family = get_family(family_lines=family_lines)172    173    recessive_variant = {'genotypes': {}}174    recessive_variant['genotypes']['proband'] = Genotype(**{'GT':'0/1'})175    176    assert check_X_dominant(177        variant = recessive_variant,178        family = family179    ) == False180def test_x_healthy_recessive_female():181    """Test a healthy heterozygote female182    183    Females needs to bo hom alt to follow pattern184    """185    family_lines = [186        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",187        "1\tproband\t0\t0\t2\t1\n"188    ]189    190    family = get_family(family_lines=family_lines)191    192    recessive_variant = {'genotypes': {}}193    recessive_variant['genotypes']['proband'] = Genotype(**{'GT':'0/1'})194    195    assert check_X_dominant(196        variant = recessive_variant,197        family = family198    ) == True199def test_x_healthy_homozygote_male():200    """Test an healthy homozygote male"""201    202    family_lines = [203        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",204        "1\tproband\t0\t0\t1\t1\n"205    ]206    207    family = get_family(family_lines=family_lines)208    209    homozygote_variant = {'genotypes': {}}210    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'1/1'})211    212    assert check_X_dominant(213        variant = homozygote_variant,214        family = family215    ) == False216def test_x_healthy_homozygote_female():217    """Test an healthy homozygote female"""218    219    family_lines = [220        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",221        "1\tproband\t0\t0\t2\t1\n"222    ]223    224    family = get_family(family_lines=family_lines)225    226    homozygote_variant = {'genotypes': {}}227    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'1/1'})228    229    assert check_X_dominant(230        variant = homozygote_variant,231        family = family232    ) == False233def test_x_healthy_male_ref_call():234    """Test an healthy ref call male"""235    236    family_lines = [237        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",238        "1\tproband\t0\t0\t1\t1\n"239    ]240    241    family = get_family(family_lines=family_lines)242    243    homozygote_variant = {'genotypes': {}}244    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'0/0'})245    246    assert check_X_dominant(247        variant = homozygote_variant,248        family = family249    ) == True250def test_x_healthy_female_ref_call():251    """Test an healthy female ref call"""252    253    family_lines = [254        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",255        "1\tproband\t0\t0\t2\t1\n"256    ]257    258    family = get_family(family_lines=family_lines)259    260    homozygote_variant = {'genotypes': {}}261    homozygote_variant['genotypes']['proband'] = Genotype(**{'GT':'0/0'})262    263    assert check_X_dominant(264        variant = homozygote_variant,265        family = family...

family.py

Source:family.py

...13        """14    res = []15    for prot, peps in peptideToProtein.items():16        for elt in peps:17            if elt.get_family() not in res:18                res.append(elt.get_family())19    return res20def assignPeptideToFamily(peptideToProtein):21    """CrÃ©e un dictionnaire qui associe Ã  chaque famille les peptides qui y apparaissent22        Args:23            peptideToProtein (dict) : les peptides associÃ©s Ã  leur protÃ©ine24        Raises:25            /26        Returns:27            dict : dictionnaire contenant en clÃ© les familles, et en valeurs les peptides appartenant Ã  ces familles28        """29    res = {}30    for prot, otherPeps in peptideToProtein.items():31        for otherP in otherPeps:32            if otherP.get_family() not in res:33                res[otherP.get_family()] = [otherP]34            else:35                if otherP not in res[otherP.get_family()]:36                    res[otherP.get_family()].append(otherP)37    return res38def familyOfPeptides(dicoPeptides):39    """CrÃ©e un dictionnaire contenant pour chaque peptide les familles auxquelles il appartient40        Args:41            dicoPeptides (dict) : les dictionnaire contenant les peptides, et les peptides identiques Ã  celui-ci en valeur42        Raises:43            /44        Returns:45            dict : dictionnaire avec les peptides en clÃ©, et les familles auxquelles ils appartiennet en valeur46        """47    dico_family = {}48    for pep, pep_list in dicoPeptides.items():49        family = []50        family.append(pep.get_family())51        for pep_identique in pep_list:52            if pep_identique.get_family() != pep.get_family():53                if pep_identique.get_family() not in family:54                    family.append(pep_identique.get_family())55        dico_family[pep] = family56    return dico_family57def seqToFamily(peptideToProtein):58    """CrÃ©e un dictionnaire qui associe Ã  chaque famille les sÃ©quences leur appartenant59        Args:60            peptideToProtein (dict) : les peptides associÃ©s Ã  leur protÃ©ine61        Raises:62            /63        Returns:64            dict : dictionnaire qui associe Ã  chaque famille les sÃ©quences leur appartenant65        """66    res = {}67    for prot, peptides in peptideToProtein.items():68        if peptides[0].get_family() not in res:69            res[peptides[0].get_family()] = [prot]70        else:71            res[peptides[0].get_family()].append(prot)72    return res73def getFamilyWithoutUnique(peptideToFamily, uniquePeptides):74    """CrÃ©e une liste contenant les familles n'ayant pas de peptide unique75    Args:76        peptideToFamily (dict) : le dictionnaire associant les peptides Ã  leur famille77        uniquePeptides (list) : la liste des peptides uniques pour une sÃ©quence78    Raises:79        /80    Returns:81        list : une liste contenant les familles n'ayant pas de peptide unique82    """83    res = list(peptideToFamily.keys())84    for pep in uniquePeptides:85        if pep.get_family() in res:86            res.remove(pep.get_family())87    return res88def where_pep_present_family(dico):89    """stock the different species the peptide appears in and make sublist of species that are part of the same family.90    Args:91        dico (dict): the dictonnary made after compare_peptide()92    Returns:93        dict: key = peptide94              values = list of sublist of species the peptide appears in (sublist = family)95    """96    dico_family = {}97    for pep, pep_list in dico.items():  # On parcours le dico98        species = []  # liste pour stocker les espÃ¨ces oÃ¹ le peptide apparaÃ®t99        species.append(pep)100        for pep_identique in pep_list:101            if pep_identique.get_nb_prot() != pep.get_nb_prot():102                species.append(pep_identique)103        family_list = []  # liste pour pouvoir constituer les sous listes d'espÃ¨ces104        species = sorted(species, key=lambda105            pep: pep.get_family())  # on range les espÃ¨ces en fonction de la famille auquelles elles appartiennent106        for k, g in itertools.groupby(species,107                                      lambda pep: pep.get_family()):  # fonction du module itertools (permet de regrouper en sous listes les elements d'une liste de dÃ©part en fonction d'un critÃ¨re, ici la famille)108            family_list.append(list(g))109        dico_family[110            pep] = family_list  # le dico avec pour chaque peptide, les espÃ¨ces regroupÃ©es en genre auquel il apparaÃ®t111    return dico_family112def unique_pep_family(dico_pep_family):113    """Let the user find the peptides that are unique to only one family (if the peptide appears only in one family).114    Args:115        dico_pep_family (dict): the dictonnary made in where_pep_present_family()116    Returns:117        list: the list containing the peptides that are unique for one family118    """119    unique_pep_family_list = []120    for pep, family_list in dico_pep_family.items():121        unique = True122        for i in range(len(family_list)):123            if i > 0:  # si la liste contient plus d'une sous liste, c'est que le peptide apparaÃ®t dans plus d'une famille donc il n'est pas unique Ã  une famille124                unique = False125                break126        if unique:127            unique_pep_family_list.append(pep)128    return sorted(unique_pep_family_list, key=lambda pep: pep.get_family())129def pretty_print_unique_peptide_family(liste, listAllFamily, output_dir):130    """Permet le formatage du fichier txt seulement pour les peptides uniques pour chaque famille131    Args:132        liste (List): the output of unique_pep_family()133        output_file (str): the name of the output file we want134        allResultsFile (str) : the name of the output file that contains all the results135    Raises:136        TypeError: if the parameters is not a list and a str137    """138    if not os.path.exists(output_dir):139        os.makedirs(output_dir)140    with open(output_dir + 'unique_pep_family.csv', 'w', newline='') as results:141        writer_family = csv.writer(results)142        writer_family.writerow(["Family", "Genus", "Protein Name", "Position", "Peptide mass", "Peptide seq"])143        for peptide in liste:144            rowToInsert = [peptide.get_family(), peptide.get_genus(), peptide.get_prot_name(), peptide.get_position(), peptide.get_mass(), peptide.get_seq()]145            writer_family.writerow(rowToInsert)146        writer_family.writerow("")147        noUnique = []148        for family in listAllFamily:149            tmp = False150            for elt in liste :151                if family == elt.get_family():152                    tmp = True153            if not tmp:154                noUnique.append(family)155        strNoUnique = ",".join(noUnique)156        writer_family.writerow(["Families that don't have a unique peptide :" + strNoUnique])157def mainFamily(dict_p, output_dir, peptidesToProtein):158    dict_f = where_pep_present_family(dict_p)159    uniquePepFamily = unique_pep_family(dict_f)160    AllFamilies = getAllFamilies(peptidesToProtein)161    # CrÃ©ation du fichier contenant les peptides uniques pour chaque famille162    pretty_print_unique_peptide_family(uniquePepFamily, AllFamilies, output_dir)163    # On cherche et renvoie les familles sans peptides uniques164    seqWithoutUniqueFamily = combinations.getSequencesWithoutUnique(peptidesToProtein, uniquePepFamily)165    return seqWithoutUniqueFamily

sim_community.py

Source:sim_community.py

...63            if not target_citizen.is_inmune():64                target_citizen.infect(step=0)65        # CreaciÃ³n de familias66        for citizen in self.citizens:67            if len(citizen.get_family()) < self.minFam:68                if self.avaible_family():69                    while len(citizen.get_family()) < self.minFam:70                        family_member = choice(self.citizens)71                        if family_member != citizen:72                            if len(family_member.get_family()) < self.minFam:73                                if not citizen in family_member.get_family():74                                    citizen.add_family_member(family_member)75                                    family_member.add_family_member(citizen)76                else:77                    self.population_is_generated = False78                    break79        80        for citizen in self.citizens:81                new_max = randrange(self.maxFam+1)82                while len(citizen.get_family()) < new_max:83                    family_member = choice(self.citizens)84                    if family_member != citizen:85                        if len(family_member.get_family()) < self.maxFam:86                            if not citizen in family_member.get_family():87                                citizen.add_family_member(family_member)88                                family_member.add_family_member(citizen)89                citizen.end_gen()90        self.update_log()91    def avaible_family(self):92        avaible_family_spaces = 093        for citizen in self.citizens:94            if len(citizen.get_family()) < self.minFam:95                avaible_family_spaces += 196                if avaible_family_spaces == 2:97                    return True98        return False99    def show_population(self):100        self.core.load_citizen_data(self.citizens)101    def take_step(self):102        self.step += 1103        # VacunaciÃ³n104        if self.step >= self.vaccines_start:105            for i in range(3):106                if self.vaccines[i].get_inventory() != 0:107                    vaccinations = randrange(self.vaccines[i].get_inventory())108                    for k in range(vaccinations):109                        not_ready = True110                        while not_ready:111                            citizen = choice(self.citizens)112                            if not citizen.is_vaccinated():113                                citizen.vaccinate(self.vaccines[i].get_vaccine_type(),self.step)114                                self.vaccines[i].use()115                                not_ready = False116        # EvoluciÃ³n117        for citizen in self.citizens:118            citizen.evolve(self.step)119        # Contacto Cercano120        for contact in range(self.contactProm):121            contact_increment = 0122            infection_increment = 0123            while True:124                citizen_a = choice(self.citizens)125                citizen_b = choice(self.citizens)126                if citizen_a != citizen_b:127                    break128            # Contacto Muy Estrecho129            if citizen_a in citizen_b.get_family():130                contact_increment = 10131                infection_increment = 5132            if randrange(100) < self.contactProb+contact_increment:133                # A infecta B134                if citizen_a.get_status():135                    if not citizen_b.is_inmune():136                        citizen_b.try_infection(self.step,infection_increment)137                # B infecta A138                if citizen_b.get_status():139                    if not citizen_a.is_inmune():140                        citizen_a.try_infection(self.step,infection_increment)141        self.update_log()142    143    def update_log(self):...

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