def __init__(self, name, get_samplelist=True, group_name=None):
assert name, "Need a name"
self.name = name
self.id = None
self.shortname = None
self.fullname = None
self.type = None
self.data_scale = None #ZS: For example log2
self.setup()
if self.type == "Temp": #Need to supply group name as input if temp trait
self.group = DatasetGroup(
self, name=group_name
) # sets self.group and self.group_id and gets genotype
else:
self.check_confidentiality()
self.retrieve_other_names()
self.group = DatasetGroup(
self) # sets self.group and self.group_id and gets genotype
self.accession_id = self.get_accession_id()
if get_samplelist == True:
self.group.get_samplelist()
self.species = species.TheSpecies(self)
def __init__(self, name, get_samplelist = True):
assert name, "Need a name"
self.name = name
self.id = None
self.shortname = None
self.fullname = None
self.type = None
self.data_scale = None #ZS: For example log2
self.setup()
self.check_confidentiality()
self.retrieve_other_names()
self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
if get_samplelist == True:
self.group.get_samplelist()
self.species = species.TheSpecies(self)
def __init__(self, start_vars, temp_uuid):
trait_db_list = [trait.strip()
for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.temp_uuid = temp_uuid
self.num_permutations = 5000
self.dataset = self.trait_list[0][1]
self.json_data = {} # The dictionary that will be used to create the json object that contains all the data needed to create the figure
self.all_sample_list = []
self.traits = []
chrnames = []
self.species = species.TheSpecies(dataset=self.trait_list[0][1])
for key in list(self.species.chromosomes.chromosomes.keys()):
chrnames.append([self.species.chromosomes.chromosomes[key].name,
self.species.chromosomes.chromosomes[key].mb_length])
for trait_db in self.trait_list:
this_trait = trait_db[0]
self.traits.append(this_trait.name)
this_sample_data = this_trait.data
for sample in this_sample_data:
if sample not in self.all_sample_list:
self.all_sample_list.append(sample)
self.sample_data = []
for trait_db in self.trait_list:
this_trait = trait_db[0]
this_sample_data = this_trait.data
this_trait_vals = []
for sample in self.all_sample_list:
if sample in this_sample_data:
this_trait_vals.append(this_sample_data[sample].value)
else:
this_trait_vals.append('')
self.sample_data.append(this_trait_vals)
self.gen_reaper_results()
lodnames = []
chr_pos = []
pos = []
markernames = []
for trait in list(self.trait_results.keys()):
lodnames.append(trait)
self.dataset.group.get_markers()
for marker in self.dataset.group.markers.markers:
chr_pos.append(marker['chr'])
pos.append(marker['Mb'])
markernames.append(marker['name'])
self.json_data['chrnames'] = chrnames
self.json_data['lodnames'] = lodnames
self.json_data['chr'] = chr_pos
self.json_data['pos'] = pos
self.json_data['markernames'] = markernames
for trait in self.trait_results:
self.json_data[trait] = self.trait_results[trait]
self.js_data = dict(
json_data=self.json_data
)
def initialize_parameters(self, start_vars):
if 'first_run' in start_vars:
self.first_run = "false"
else:
self.first_run = "true"
self.allele_list = []
self.variant_type = "SNP"
if 'variant' in start_vars:
self.variant_type = start_vars['variant']
self.species_name = "Mouse"
self.species_id = 1
if 'species' in start_vars:
self.species_name = start_vars['species']
if self.species_name.capitalize() == "Rat":
self.species_id = 2
self.mouse_chr_list = []
self.rat_chr_list = []
mouse_species_ob = species.TheSpecies(species_name="Mouse")
for key in mouse_species_ob.chromosomes.chromosomes:
self.mouse_chr_list.append(
mouse_species_ob.chromosomes.chromosomes[key].name)
rat_species_ob = species.TheSpecies(species_name="Rat")
for key in rat_species_ob.chromosomes.chromosomes:
self.rat_chr_list.append(
rat_species_ob.chromosomes.chromosomes[key].name)
if self.species_id == 1:
self.this_chr_list = self.mouse_chr_list
else:
self.this_chr_list = self.rat_chr_list
if self.first_run == "true":
self.chr = "19"
self.start_mb = 30.1
self.end_mb = 30.12
else:
if 'gene_name' in start_vars:
if start_vars['gene_name'] != "":
self.gene_name = start_vars['gene_name']
else:
self.gene_name = ""
self.chr = start_vars['chr']
try:
self.start_mb = float(start_vars['start_mb'])
self.end_mb = float(start_vars['end_mb'])
except:
self.start_mb = 0.0
self.end_mb = 0.0
else:
try:
self.chr = start_vars['chr']
self.start_mb = float(start_vars['start_mb'])
self.end_mb = float(start_vars['end_mb'])
except:
self.chr = "1"
self.start_mb = 0.0
self.end_mb = 0.0
self.limit_strains = "true"
if self.first_run == "false":
if 'limit_strains' not in start_vars:
self.limit_strains = "false"
else:
if start_vars['limit_strains'] == "false":
self.limit_strains = "false"
self.chosen_strains_mouse = [
"C57BL/6J", "DBA/2J", "A/J", "129S1/SvImJ", "NOD/ShiLtJ",
"NZO/HlLtJ", "WSB/EiJ", "PWK/PhJ", "CAST/EiJ"
]
self.chosen_strains_rat = ["BN", "F344", "WLI", "WMI"]
if 'chosen_strains_mouse' in start_vars:
self.chosen_strains_mouse = start_vars[
'chosen_strains_mouse'].split(",")
if 'chosen_strains_rat' in start_vars:
self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(
",")
if self.species_id == 1:
self.chosen_strains = self.chosen_strains_mouse
else:
self.chosen_strains = self.chosen_strains_rat
self.domain = "All"
if 'domain' in start_vars:
self.domain = start_vars['domain']
self.function = "All"
if 'function' in start_vars:
self.function = start_vars['function']
self.source = "All"
if 'source' in start_vars:
self.source = start_vars['source']
self.criteria = ">="
if 'criteria' in start_vars:
self.criteria = start_vars['criteria']
self.score = 0.0
if 'score' in start_vars:
self.score = start_vars['score']
self.redundant = "false"
if self.first_run == "false" and 'redundant' in start_vars:
self.redundant = "true"
self.diff_alleles = "true"
if self.first_run == "false":
if 'diff_alleles' not in start_vars:
self.diff_alleles = "false"
else:
if start_vars['diff_alleles'] == "false":
self.diff_alleles = "false"