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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 """Crée un dictionnaire qui associe à chaque famille les peptides qui y apparaissent22 Args:23 peptideToProtein (dict) : les peptides associés à leur protéine24 Raises:25 /26 Returns:27 dict : dictionnaire contenant en clé les familles, et en valeurs les peptides appartenant à 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 """Crée un dictionnaire contenant pour chaque peptide les familles auxquelles il appartient40 Args:41 dicoPeptides (dict) : les dictionnaire contenant les peptides, et les peptides identiques à celui-ci en valeur42 Raises:43 /44 Returns:45 dict : dictionnaire avec les peptides en clé, 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 """Crée un dictionnaire qui associe à chaque famille les séquences leur appartenant59 Args:60 peptideToProtein (dict) : les peptides associés à leur protéine61 Raises:62 /63 Returns:64 dict : dictionnaire qui associe à chaque famille les séquences 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 """Crée une liste contenant les familles n'ayant pas de peptide unique75 Args:76 peptideToFamily (dict) : le dictionnaire associant les peptides à leur famille77 uniquePeptides (list) : la liste des peptides uniques pour une séquence78 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 espèces où le peptide apparaît99 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'espèces104 species = sorted(species, key=lambda105 pep: pep.get_family()) # on range les espèces 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 départ en fonction d'un critère, ici la famille)108 family_list.append(list(g))109 dico_family[110 pep] = family_list # le dico avec pour chaque peptide, les espèces regroupées en genre auquel il apparaît111 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 apparaît dans plus d'une famille donc il n'est pas unique à 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 # Création 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 # Creación 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 # Vacunación104 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 # Evolución117 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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