Submodules

• src.features.affymetrix
  • read_Manifest()
  • read_affymetrixRow()
  • search_manifactured_date()
  • search_n_samples()
  • search_n_snps()
• src.data.common
  • AssemblyConf
    • AssemblyConf.imported_from
    • AssemblyConf.version
  • deal_with_datasets()
  • deal_with_sex_and_alias()
  • fetch_and_check_dataset()
  • get_sample_species()
  • get_variant_species()
  • new_variant()
  • pandas_open()
  • update_affymetrix_record()
  • update_chip_name()
  • update_location()
  • update_probesets()
  • update_rs_id()
  • update_sequence()
  • update_variant()
• src.features.dbsnp
  • DBSNP
    • DBSNP.__init__()
    • DBSNP.ass_component()
    • DBSNP.ass_maploc()
    • DBSNP.ass_snpstat()
    • DBSNP.clean_tag()
    • DBSNP.config
    • DBSNP.process_element()
    • DBSNP.record_assembly()
    • DBSNP.record_create()
    • DBSNP.record_exemplar()
    • DBSNP.record_observed()
    • DBSNP.record_ss()
    • DBSNP.record_update()
    • DBSNP.recurse_children()
    • DBSNP.ss_observed()
    • DBSNP.ss_seq3()
    • DBSNP.ss_seq5()
    • DBSNP.to_dict()
  • process_rs_elem()
  • read_dbSNP()
  • search_chip_snps()
• src.features.illumina
  • IlluSNP
    • IlluSNP.__init__()
    • IlluSNP.findSNP()
    • IlluSNP.fromSequence()
    • IlluSNP.isUnambiguous()
    • IlluSNP.toTop()
  • IlluSNPException
    • IlluSNPException.__init__()
  • read_Manifest()
  • read_illuminaRow()
  • read_snpList()
  • read_snpMap()
  • search_manifactured_date()
  • skip_lines()
  • skip_until_section()
  • sniff_file()
• src.features.plinkio
  • AffyPlinkIO
    • AffyPlinkIO
  • AffyReportIO
    • AffyReportIO
  • BinaryPlinkIO
    • BinaryPlinkIO
  • MapRecord
    • MapRecord
  • FakePedMixin
    • FakePedMixin
  • IlluminaReportIO
    • IlluminaReportIO
  • SmarterMixin
    • SmarterMixin
  • TextPlinkIO
    • TextPlinkIO
  • plink_binary_exists
    • plinkio.plink_binary_exists()
• src.features.smarterdb
  • Breed
    • Breed.DoesNotExist
    • Breed.MultipleObjectsReturned
    • Breed.aliases
    • Breed.code
    • Breed.id
    • Breed.n_individuals
    • Breed.name
    • Breed.objects
    • Breed.species
  • BreedAlias
    • BreedAlias.country
    • BreedAlias.dataset
    • BreedAlias.fid
  • Consequence
  • Counter
    • Counter.DoesNotExist
    • Counter.MultipleObjectsReturned
    • Counter.id
    • Counter.objects
    • Counter.sequence_value
  • Country
    • Country.DoesNotExist
    • Country.MultipleObjectsReturned
    • Country.__init__()
    • Country.alpha_2
    • Country.alpha_3
    • Country.id
    • Country.name
    • Country.numeric
    • Country.objects
    • Country.official_name
    • Country.species
  • Dataset
    • Dataset.DoesNotExist
    • Dataset.MultipleObjectsReturned
    • Dataset.breed
    • Dataset.chip_name
    • Dataset.contents
    • Dataset.country
    • Dataset.doi
    • Dataset.file
    • Dataset.gene_array
    • Dataset.id
    • Dataset.n_of_individuals
    • Dataset.n_of_records
    • Dataset.objects
    • Dataset.partner
    • Dataset.result_dir
    • Dataset.size_
    • Dataset.species
    • Dataset.trait
    • Dataset.type_
    • Dataset.uploader
    • Dataset.working_dir
  • Location
    • Location.__init__()
    • Location.ab2top()
    • Location.affy2top()
    • Location.affymetrix_ab
    • Location.alleles
    • Location.chrom
    • Location.consequences
    • Location.date
    • Location.forward2top()
    • Location.illumina
    • Location.illumina2top()
    • Location.illumina_forward
    • Location.illumina_strand
    • Location.illumina_top
    • Location.imported_from
    • Location.is_ab()
    • Location.is_affymetrix()
    • Location.is_forward()
    • Location.is_illumina()
    • Location.is_top()
    • Location.position
    • Location.ss_id
    • Location.strand
    • Location.top2forward()
    • Location.version
  • Phenotype
    • Phenotype.chest_girth
    • Phenotype.height
    • Phenotype.length
    • Phenotype.purpose
  • Probeset
    • Probeset.chip_name
    • Probeset.probeset_id
  • SAMPLETYPE
    • SAMPLETYPE.BACKGROUND
    • SAMPLETYPE.FOREGROUND
  • SEX
    • SEX.FEMALE
    • SEX.MALE
    • SEX.UNKNOWN
    • SEX.from_string()
  • SampleGoat
    • SampleGoat.DoesNotExist
    • SampleGoat.MultipleObjectsReturned
    • SampleGoat.father_id
    • SampleGoat.id
    • SampleGoat.mother_id
    • SampleGoat.objects
    • SampleGoat.species
    • SampleGoat.species_class
  • SampleSheep
    • SampleSheep.DoesNotExist
    • SampleSheep.MultipleObjectsReturned
    • SampleSheep.father_id
    • SampleSheep.id
    • SampleSheep.mother_id
    • SampleSheep.objects
    • SampleSheep.species
    • SampleSheep.species_class
  • SampleSpecies
    • SampleSpecies.alias
    • SampleSpecies.breed
    • SampleSpecies.breed_code
    • SampleSpecies.chip_name
    • SampleSpecies.country
    • SampleSpecies.dataset
    • SampleSpecies.locations
    • SampleSpecies.metadata
    • SampleSpecies.original_id
    • SampleSpecies.phenotype
    • SampleSpecies.save()
    • SampleSpecies.sex
    • SampleSpecies.smarter_id
    • SampleSpecies.species_class
    • SampleSpecies.type_
  • SmarterDBException
  • SmarterInfo
    • SmarterInfo.DoesNotExist
    • SmarterInfo.MultipleObjectsReturned
    • SmarterInfo.id
    • SmarterInfo.last_updated
    • SmarterInfo.objects
    • SmarterInfo.plink_specie_opt
    • SmarterInfo.version
    • SmarterInfo.working_assemblies
  • SupportedChip
    • SupportedChip.DoesNotExist
    • SupportedChip.MultipleObjectsReturned
    • SupportedChip.id
    • SupportedChip.manufacturer
    • SupportedChip.n_of_snps
    • SupportedChip.name
    • SupportedChip.objects
    • SupportedChip.species
  • VariantGoat
    • VariantGoat.DoesNotExist
    • VariantGoat.MultipleObjectsReturned
    • VariantGoat.id
    • VariantGoat.objects
  • VariantSheep
    • VariantSheep.DoesNotExist
    • VariantSheep.MultipleObjectsReturned
    • VariantSheep.id
    • VariantSheep.objects
  • VariantSpecies
    • VariantSpecies.affy_snp_id
    • VariantSpecies.chip_name
    • VariantSpecies.cust_id
    • VariantSpecies.get_location()
    • VariantSpecies.get_location_index()
    • VariantSpecies.illumina_top
    • VariantSpecies.locations
    • VariantSpecies.name
    • VariantSpecies.probesets
    • VariantSpecies.rs_id
    • VariantSpecies.save()
    • VariantSpecies.sender
    • VariantSpecies.sequence
  • complement()
  • getNextSequenceValue()
  • getSmarterId()
  • get_or_create_breed()
  • get_or_create_sample()
  • get_sample_type()
  • global_connection()
• src.features.snpchimp
  • clean_chrom()
  • read_snpChimp()
• src.features.utils
  • TqdmToLogger
    • TqdmToLogger.__init__()
    • TqdmToLogger.buf
    • TqdmToLogger.flush()
    • TqdmToLogger.level
    • TqdmToLogger.logger
    • TqdmToLogger.write()
  • UnknownCountry
    • UnknownCountry.__init__()
  • camelCase()
  • find_duplicates()
  • get_interim_dir()
  • get_processed_dir()
  • get_project_dir()
  • get_raw_dir()
  • sanitize()
  • skip_comments()
  • text_or_gzip_open()