SMARTER Database
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Loading variants into database
The Data Import Process
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Index
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Symbols
--additional_column
src/data/import_phenotypes.py command line option
--alias
src/data/add_breed.py command line option
--alias_column
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
src/data/import_samples.py command line option
--alleles_column
src/data/import_isgc.py command line option
--assembly
src/data/import_from_affymetrix.py command line option
src/data/import_from_illumina.py command line option
src/data/import_from_plink.py command line option
src/data/merge_datasets.py command line option
src/data/SNPconvert.py command line option
--bfile
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--breed_code
src/data/import_from_affymetrix.py command line option
src/data/import_from_illumina.py command line option
--breed_column
src/data/import_breeds.py command line option
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
--chest_girth_column
src/data/import_phenotypes.py command line option
--chip_file
src/data/import_snpchips.py command line option
--chip_name
src/data/import_affymetrix.py command line option
src/data/import_from_affymetrix.py command line option
src/data/import_from_illumina.py command line option
src/data/import_from_plink.py command line option
src/data/import_manifest.py command line option
src/data/import_samples.py command line option
src/data/SNPconvert.py command line option
--chrom_column
src/data/import_iggc.py command line option
src/data/import_isgc.py command line option
--code
src/data/add_breed.py command line option
--code_all
src/data/import_samples.py command line option
--code_column
src/data/import_breeds.py command line option
src/data/import_samples.py command line option
--coding
src/data/import_from_affymetrix.py command line option
src/data/import_from_illumina.py command line option
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--column
src/data/import_multiple_phenotypes.py command line option
--country_all
src/data/import_samples.py command line option
--country_column
src/data/import_breeds.py command line option
src/data/import_samples.py command line option
--create_samples
src/data/import_from_affymetrix.py command line option
src/data/import_from_illumina.py command line option
src/data/import_from_plink.py command line option
--datafile
src/data/import_breeds.py command line option
src/data/import_iggc.py command line option
src/data/import_isgc.py command line option
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
src/data/import_samples.py command line option
--dataset
src/data/add_breed.py command line option
src/data/import_from_affymetrix.py command line option
src/data/import_from_illumina.py command line option
src/data/import_from_plink.py command line option
--date
src/data/import_iggc.py command line option
src/data/import_isgc.py command line option
--dst_dataset
src/data/import_breeds.py command line option
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
src/data/import_samples.py command line option
--entry_column
src/data/import_iggc.py command line option
src/data/import_isgc.py command line option
--fid_column
src/data/import_breeds.py command line option
--file
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--force_update
src/data/import_iggc.py command line option
src/data/import_isgc.py command line option
--height_column
src/data/import_phenotypes.py command line option
--id_column
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
src/data/import_samples.py command line option
--ignore_coding_errors
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--imported_from
src/data/import_dbsnp.py command line option
--input_dir
src/data/import_dbsnp.py command line option
--latitude_column
src/data/import_metadata.py command line option
--length_column
src/data/import_phenotypes.py command line option
--longitude_column
src/data/import_metadata.py command line option
--manifest
src/data/import_affymetrix.py command line option
src/data/import_manifest.py command line option
--max_samples
src/data/import_from_affymetrix.py command line option
--metadata_column
src/data/import_metadata.py command line option
--na_values
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
--name
src/data/add_breed.py command line option
--notes_column
src/data/import_metadata.py command line option
--pattern
src/data/import_dbsnp.py command line option
--pos_column
src/data/import_iggc.py command line option
src/data/import_isgc.py command line option
--prefix
src/data/import_from_affymetrix.py command line option
--purpose_column
src/data/import_phenotypes.py command line option
--report
src/data/import_from_affymetrix.py command line option
src/data/import_from_illumina.py command line option
src/data/SNPconvert.py command line option
--results_dir
src/data/SNPconvert.py command line option
--rs_column
src/data/import_iggc.py command line option
--sample_field
src/data/import_from_affymetrix.py command line option
src/data/import_from_plink.py command line option
--search_by_positions
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--search_field
src/data/import_from_affymetrix.py command line option
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--sender
src/data/import_dbsnp.py command line option
src/data/import_manifest.py command line option
--sequence_column
src/data/import_iggc.py command line option
--sex_column
src/data/import_metadata.py command line option
src/data/import_samples.py command line option
--sheet_name
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
--skip_coordinate_check
src/data/import_from_affymetrix.py command line option
--skip_missing_alias
src/data/import_samples.py command line option
--snpchimp
src/data/import_snpchimp.py command line option
--snpfile
src/data/import_from_illumina.py command line option
src/data/SNPconvert.py command line option
--species
src/data/SNPconvert.py command line option
--species_all
src/data/import_samples.py command line option
--species_class
src/data/add_breed.py command line option
src/data/import_affymetrix.py command line option
src/data/import_breeds.py command line option
src/data/import_dbsnp.py command line option
src/data/import_manifest.py command line option
src/data/import_snpchimp.py command line option
src/data/merge_datasets.py command line option
--species_column
src/data/import_metadata.py command line option
src/data/import_samples.py command line option
--src_dataset
src/data/import_breeds.py command line option
src/data/import_metadata.py command line option
src/data/import_multiple_phenotypes.py command line option
src/data/import_phenotypes.py command line option
src/data/import_samples.py command line option
--src_imported_from
src/data/import_from_affymetrix.py command line option
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--src_version
src/data/import_from_affymetrix.py command line option
src/data/import_from_plink.py command line option
src/data/SNPconvert.py command line option
--strand_column
src/data/import_iggc.py command line option
--types
src/data/import_datasets.py command line option
--version
src/data/import_affymetrix.py command line option
src/data/import_dbsnp.py command line option
src/data/import_iggc.py command line option
src/data/import_isgc.py command line option
src/data/import_manifest.py command line option
src/data/import_snpchimp.py command line option
_
__init__() (src.features.dbsnp.DBSNP method)
(src.features.illumina.IlluSNP method)
(src.features.illumina.IlluSNPException method)
(src.features.plinkio.AffyReportIO method)
(src.features.plinkio.BinaryPlinkIO method)
(src.features.plinkio.IlluminaReportIO method)
(src.features.plinkio.MapRecord method)
(src.features.plinkio.TextPlinkIO method)
(src.features.smarterdb.Country method)
(src.features.smarterdb.Location method)
(src.features.utils.TqdmToLogger method)
(src.features.utils.UnknownCountry method)
A
ab2top() (src.features.smarterdb.Location method)
affy2top() (src.features.smarterdb.Location method)
affy_snp_id (src.features.smarterdb.VariantSpecies attribute)
affymetrix_ab (src.features.smarterdb.Location attribute)
AffyPlinkIO (class in src.features.plinkio)
AffyReportIO (class in src.features.plinkio)
alias (src.features.smarterdb.SampleSpecies attribute)
aliases (src.features.smarterdb.Breed attribute)
alleles (src.features.smarterdb.Location attribute)
alpha_2 (src.features.smarterdb.Country attribute)
alpha_3 (src.features.smarterdb.Country attribute)
ass_component() (src.features.dbsnp.DBSNP method)
ass_maploc() (src.features.dbsnp.DBSNP method)
ass_snpstat() (src.features.dbsnp.DBSNP method)
AssemblyConf (class in src.data.common)
B
BACKGROUND (src.features.smarterdb.SAMPLETYPE attribute)
BinaryPlinkIO (class in src.features.plinkio)
Breed (class in src.features.smarterdb)
breed (src.features.smarterdb.Dataset attribute)
(src.features.smarterdb.SampleSpecies attribute)
Breed.DoesNotExist
Breed.MultipleObjectsReturned
breed_code (src.features.smarterdb.SampleSpecies attribute)
BreedAlias (class in src.features.smarterdb)
buf (src.features.utils.TqdmToLogger attribute)
C
camelCase() (in module src.features.utils)
chest_girth (src.features.smarterdb.Phenotype attribute)
chip_name (src.features.plinkio.SmarterMixin attribute)
(src.features.smarterdb.Dataset attribute)
(src.features.smarterdb.Probeset attribute)
(src.features.smarterdb.SampleSpecies attribute)
(src.features.smarterdb.VariantSpecies attribute)
chrom (src.features.plinkio.MapRecord attribute)
(src.features.smarterdb.Location attribute)
clean_chrom() (in module src.features.snpchimp)
clean_tag() (src.features.dbsnp.DBSNP class method)
cm (src.features.plinkio.MapRecord attribute)
code (src.features.smarterdb.Breed attribute)
complement() (in module src.features.smarterdb)
config (src.features.dbsnp.DBSNP attribute)
Consequence (class in src.features.smarterdb)
consequences (src.features.smarterdb.Location attribute)
contents (src.features.smarterdb.Dataset attribute)
Counter (class in src.features.smarterdb)
Counter.DoesNotExist
Counter.MultipleObjectsReturned
Country (class in src.features.smarterdb)
country (src.features.smarterdb.BreedAlias attribute)
(src.features.smarterdb.Dataset attribute)
(src.features.smarterdb.SampleSpecies attribute)
Country.DoesNotExist
Country.MultipleObjectsReturned
cust_id (src.features.smarterdb.VariantSpecies attribute)
D
Dataset (class in src.features.smarterdb)
dataset (src.features.smarterdb.BreedAlias attribute)
(src.features.smarterdb.SampleSpecies attribute)
Dataset.DoesNotExist
Dataset.MultipleObjectsReturned
date (src.features.smarterdb.Location attribute)
DBSNP (class in src.features.dbsnp)
deal_with_datasets() (in module src.data.common)
deal_with_sex_and_alias() (in module src.data.common)
delimiter (src.features.plinkio.AffyReportIO attribute)
doi (src.features.smarterdb.Dataset attribute)
dst_locations (src.features.plinkio.SmarterMixin attribute)
F
FakePedMixin (class in src.features.plinkio)
father_id (src.features.smarterdb.SampleGoat attribute)
(src.features.smarterdb.SampleSheep attribute)
FEMALE (src.features.smarterdb.SEX attribute)
fetch_and_check_dataset() (in module src.data.common)
fetch_coordinates() (src.features.plinkio.AffyReportIO method)
(src.features.plinkio.SmarterMixin method)
fetch_coordinates_by_positions() (src.features.plinkio.SmarterMixin method)
fid (src.features.smarterdb.BreedAlias attribute)
file (src.features.smarterdb.Dataset attribute)
filtered (src.features.plinkio.SmarterMixin attribute)
find_duplicates() (in module src.features.utils)
findSNP() (src.features.illumina.IlluSNP method)
flush() (src.features.utils.TqdmToLogger method)
FOREGROUND (src.features.smarterdb.SAMPLETYPE attribute)
forward2top() (src.features.smarterdb.Location method)
from_string() (src.features.smarterdb.SEX class method)
fromSequence() (src.features.illumina.IlluSNP method)
G
gene_array (src.features.smarterdb.Dataset attribute)
get_interim_dir() (in module src.features.utils)
get_location() (src.features.smarterdb.VariantSpecies method)
get_location_index() (src.features.smarterdb.VariantSpecies method)
get_or_create_breed() (in module src.features.smarterdb)
get_or_create_sample() (in module src.features.smarterdb)
(src.features.plinkio.SmarterMixin method)
get_processed_dir() (in module src.features.utils)
get_project_dir() (in module src.features.utils)
get_raw_dir() (in module src.features.utils)
get_sample_species() (in module src.data.common)
get_sample_type() (in module src.features.smarterdb)
get_samples() (src.features.plinkio.AffyPlinkIO method)
(src.features.plinkio.AffyReportIO method)
(src.features.plinkio.BinaryPlinkIO method)
(src.features.plinkio.IlluminaReportIO method)
(src.features.plinkio.TextPlinkIO method)
get_variant_species() (in module src.data.common)
getNextSequenceValue() (in module src.features.smarterdb)
getSmarterId() (in module src.features.smarterdb)
global_connection() (in module src.features.smarterdb)
H
header (src.features.plinkio.AffyReportIO attribute)
height (src.features.smarterdb.Phenotype attribute)
I
id (src.features.smarterdb.Breed attribute)
(src.features.smarterdb.Counter attribute)
(src.features.smarterdb.Country attribute)
(src.features.smarterdb.Dataset attribute)
(src.features.smarterdb.SampleGoat attribute)
(src.features.smarterdb.SampleSheep attribute)
(src.features.smarterdb.SmarterInfo attribute)
(src.features.smarterdb.SupportedChip attribute)
(src.features.smarterdb.VariantGoat attribute)
(src.features.smarterdb.VariantSheep attribute)
illumina (src.features.smarterdb.Location attribute)
illumina2top() (src.features.smarterdb.Location method)
illumina_forward (src.features.smarterdb.Location attribute)
illumina_strand (src.features.smarterdb.Location attribute)
illumina_top (src.features.smarterdb.Location property)
(src.features.smarterdb.VariantSpecies attribute)
IlluminaReportIO (class in src.features.plinkio)
IlluSNP (class in src.features.illumina)
IlluSNPException
imported_from (src.data.common.AssemblyConf attribute)
(src.features.smarterdb.Location attribute)
INPUT_FILEPATH
src/data/import_datasets.py command line option
is_ab() (src.features.smarterdb.Location method)
is_affymetrix() (src.features.smarterdb.Location method)
is_forward() (src.features.smarterdb.Location method)
is_illumina() (src.features.smarterdb.Location method)
is_top() (src.features.smarterdb.Location method)
isUnambiguous() (src.features.illumina.IlluSNP method)
L
last_updated (src.features.smarterdb.SmarterInfo attribute)
length (src.features.smarterdb.Phenotype attribute)
level (src.features.utils.TqdmToLogger attribute)
Location (class in src.features.smarterdb)
locations (src.features.smarterdb.SampleSpecies attribute)
(src.features.smarterdb.VariantSpecies attribute)
logger (src.features.utils.TqdmToLogger attribute)
M
make_query_args() (src.features.plinkio.SmarterMixin method)
make_query_kwargs() (src.features.plinkio.SmarterMixin method)
MALE (src.features.smarterdb.SEX attribute)
manifacturer (src.features.smarterdb.SupportedChip attribute)
mapdata (src.features.plinkio.SmarterMixin attribute)
mapfile (src.features.plinkio.TextPlinkIO attribute)
MapRecord (class in src.features.plinkio)
metadata (src.features.smarterdb.SampleSpecies attribute)
module
src.data.common
src.features.affymetrix
src.features.dbsnp
src.features.illumina
src.features.smarterdb
src.features.snpchimp
src.features.utils
mother_id (src.features.smarterdb.SampleGoat attribute)
(src.features.smarterdb.SampleSheep attribute)
N
n_individuals (src.features.smarterdb.Breed attribute)
n_of_individuals (src.features.smarterdb.Dataset attribute)
n_of_records (src.features.smarterdb.Dataset attribute)
n_of_snps (src.features.smarterdb.SupportedChip attribute)
n_samples (src.features.plinkio.AffyReportIO attribute)
name (src.features.plinkio.MapRecord attribute)
(src.features.smarterdb.Breed attribute)
(src.features.smarterdb.Country attribute)
(src.features.smarterdb.SupportedChip attribute)
(src.features.smarterdb.VariantSpecies attribute)
new_variant() (in module src.data.common)
numeric (src.features.smarterdb.Country attribute)
O
objects (src.features.smarterdb.Breed attribute)
(src.features.smarterdb.Counter attribute)
(src.features.smarterdb.Country attribute)
(src.features.smarterdb.Dataset attribute)
(src.features.smarterdb.SampleGoat attribute)
(src.features.smarterdb.SampleSheep attribute)
(src.features.smarterdb.SmarterInfo attribute)
(src.features.smarterdb.SupportedChip attribute)
(src.features.smarterdb.VariantGoat attribute)
(src.features.smarterdb.VariantSheep attribute)
official_name (src.features.smarterdb.Country attribute)
original_id (src.features.smarterdb.SampleSpecies attribute)
P
pandas_open() (in module src.data.common)
partner (src.features.smarterdb.Dataset attribute)
peddata (src.features.plinkio.AffyReportIO attribute)
pedfile (src.features.plinkio.TextPlinkIO attribute)
Phenotype (class in src.features.smarterdb)
phenotype (src.features.smarterdb.SampleSpecies attribute)
plink_binary_exists() (src.features.plinkio method)
plink_file (src.features.plinkio.BinaryPlinkIO attribute)
plink_specie_opt (src.features.smarterdb.SmarterInfo attribute)
position (src.features.plinkio.MapRecord attribute)
(src.features.smarterdb.Location attribute)
prefix (src.features.plinkio.BinaryPlinkIO property)
Probeset (class in src.features.smarterdb)
probeset_id (src.features.smarterdb.Probeset attribute)
probesets (src.features.smarterdb.VariantSpecies attribute)
process_element() (src.features.dbsnp.DBSNP method)
process_rs_elem() (in module src.features.dbsnp)
purpose (src.features.smarterdb.Phenotype attribute)
R
read_affymetrixRow() (in module src.features.affymetrix)
read_dbSNP() (in module src.features.dbsnp)
read_genotype_method (src.features.plinkio.SmarterMixin attribute)
read_illuminaRow() (in module src.features.illumina)
read_Manifest() (in module src.features.affymetrix)
(in module src.features.illumina)
read_mapfile() (src.features.plinkio.BinaryPlinkIO method)
(src.features.plinkio.TextPlinkIO method)
read_peddata() (src.features.plinkio.AffyReportIO method)
read_pedfile() (src.features.plinkio.AffyPlinkIO method)
(src.features.plinkio.BinaryPlinkIO method)
(src.features.plinkio.TextPlinkIO method)
read_reportfile() (src.features.plinkio.AffyReportIO method)
(src.features.plinkio.IlluminaReportIO method)
read_snpChimp() (in module src.features.snpchimp)
read_snpfile() (src.features.plinkio.IlluminaReportIO method)
read_snpList() (in module src.features.illumina)
read_snpMap() (in module src.features.illumina)
record_assembly() (src.features.dbsnp.DBSNP method)
record_create() (src.features.dbsnp.DBSNP method)
record_exemplar() (src.features.dbsnp.DBSNP method)
record_observed() (src.features.dbsnp.DBSNP method)
record_ss() (src.features.dbsnp.DBSNP method)
record_update() (src.features.dbsnp.DBSNP method)
recurse_children() (src.features.dbsnp.DBSNP method)
report (src.features.plinkio.AffyReportIO attribute)
(src.features.plinkio.IlluminaReportIO attribute)
result_dir (src.features.smarterdb.Dataset property)
rs_id (src.features.smarterdb.VariantSpecies attribute)
S
SampleGoat (class in src.features.smarterdb)
SampleGoat.DoesNotExist
SampleGoat.MultipleObjectsReturned
SampleSheep (class in src.features.smarterdb)
SampleSheep.DoesNotExist
SampleSheep.MultipleObjectsReturned
SampleSpecies (class in src.features.smarterdb)
(src.features.plinkio.SmarterMixin attribute)
SAMPLETYPE (class in src.features.smarterdb)
sanitize() (in module src.features.utils)
save() (src.features.smarterdb.SampleSpecies method)
(src.features.smarterdb.VariantSpecies method)
search_breed() (src.features.plinkio.FakePedMixin method)
(src.features.plinkio.SmarterMixin method)
search_chip_snps() (in module src.features.dbsnp)
search_country() (src.features.plinkio.SmarterMixin method)
search_fid() (src.features.plinkio.FakePedMixin method)
search_manifactured_date() (in module src.features.affymetrix)
(in module src.features.illumina)
search_n_samples() (in module src.features.affymetrix)
search_n_snps() (in module src.features.affymetrix)
sender (src.features.smarterdb.VariantSpecies attribute)
sequence (src.features.smarterdb.VariantSpecies attribute)
sequence_value (src.features.smarterdb.Counter attribute)
SEX (class in src.features.smarterdb)
sex (src.features.smarterdb.SampleSpecies attribute)
size_ (src.features.smarterdb.Dataset attribute)
skip_comments() (in module src.features.utils)
skip_index() (src.features.plinkio.SmarterMixin method)
skip_lines() (in module src.features.illumina)
skip_until_section() (in module src.features.illumina)
smarter_id (src.features.smarterdb.SampleSpecies attribute)
SmarterDBException
SmarterInfo (class in src.features.smarterdb)
SmarterInfo.DoesNotExist
SmarterInfo.MultipleObjectsReturned
SmarterMixin (class in src.features.plinkio)
sniff_file() (in module src.features.illumina)
snpfile (src.features.plinkio.IlluminaReportIO attribute)
species (src.features.plinkio.SmarterMixin property)
(src.features.smarterdb.Breed attribute)
(src.features.smarterdb.Country attribute)
(src.features.smarterdb.Dataset attribute)
(src.features.smarterdb.SampleGoat attribute)
(src.features.smarterdb.SampleSheep attribute)
(src.features.smarterdb.SupportedChip attribute)
species_class (src.features.smarterdb.SampleGoat attribute)
(src.features.smarterdb.SampleSheep attribute)
(src.features.smarterdb.SampleSpecies attribute)
src.data.common
module
src.features.affymetrix
module
src.features.dbsnp
module
src.features.illumina
module
src.features.smarterdb
module
src.features.snpchimp
module
src.features.utils
module
src/data/add_breed.py command line option
--alias
--code
--dataset
--name
--species_class
src/data/import_affymetrix.py command line option
--chip_name
--manifest
--species_class
--version
src/data/import_breeds.py command line option
--breed_column
--code_column
--country_column
--datafile
--dst_dataset
--fid_column
--species_class
--src_dataset
src/data/import_datasets.py command line option
--types
INPUT_FILEPATH
src/data/import_dbsnp.py command line option
--imported_from
--input_dir
--pattern
--sender
--species_class
--version
src/data/import_from_affymetrix.py command line option
--assembly
--breed_code
--chip_name
--coding
--create_samples
--dataset
--max_samples
--prefix
--report
--sample_field
--search_field
--skip_coordinate_check
--src_imported_from
--src_version
src/data/import_from_illumina.py command line option
--assembly
--breed_code
--chip_name
--coding
--create_samples
--dataset
--report
--snpfile
src/data/import_from_plink.py command line option
--assembly
--bfile
--chip_name
--coding
--create_samples
--dataset
--file
--ignore_coding_errors
--sample_field
--search_by_positions
--search_field
--src_imported_from
--src_version
src/data/import_iggc.py command line option
--chrom_column
--datafile
--date
--entry_column
--force_update
--pos_column
--rs_column
--sequence_column
--strand_column
--version
src/data/import_isgc.py command line option
--alleles_column
--chrom_column
--datafile
--date
--entry_column
--force_update
--pos_column
--version
src/data/import_manifest.py command line option
--chip_name
--manifest
--sender
--species_class
--version
src/data/import_metadata.py command line option
--alias_column
--breed_column
--datafile
--dst_dataset
--id_column
--latitude_column
--longitude_column
--metadata_column
--na_values
--notes_column
--sex_column
--sheet_name
--species_column
--src_dataset
src/data/import_multiple_phenotypes.py command line option
--alias_column
--breed_column
--column
--datafile
--dst_dataset
--id_column
--na_values
--sheet_name
--src_dataset
src/data/import_phenotypes.py command line option
--additional_column
--alias_column
--breed_column
--chest_girth_column
--datafile
--dst_dataset
--height_column
--id_column
--length_column
--na_values
--purpose_column
--sheet_name
--src_dataset
src/data/import_samples.py command line option
--alias_column
--chip_name
--code_all
--code_column
--country_all
--country_column
--datafile
--dst_dataset
--id_column
--sex_column
--skip_missing_alias
--species_all
--species_column
--src_dataset
src/data/import_snpchimp.py command line option
--snpchimp
--species_class
--version
src/data/import_snpchips.py command line option
--chip_file
src/data/merge_datasets.py command line option
--assembly
--species_class
src/data/SNPconvert.py command line option
--assembly
--bfile
--chip_name
--coding
--file
--ignore_coding_errors
--report
--results_dir
--search_by_positions
--search_field
--snpfile
--species
--src_imported_from
--src_version
src_locations (src.features.plinkio.SmarterMixin attribute)
ss_id (src.features.smarterdb.Location attribute)
ss_observed() (src.features.dbsnp.DBSNP method)
ss_seq3() (src.features.dbsnp.DBSNP method)
ss_seq5() (src.features.dbsnp.DBSNP method)
strand (src.features.smarterdb.Location attribute)
SupportedChip (class in src.features.smarterdb)
SupportedChip.DoesNotExist
SupportedChip.MultipleObjectsReturned
T
text_or_gzip_open() (in module src.features.utils)
TextPlinkIO (class in src.features.plinkio)
to_dict() (src.features.dbsnp.DBSNP method)
toTop() (src.features.illumina.IlluSNP method)
TqdmToLogger (class in src.features.utils)
trait (src.features.smarterdb.Dataset attribute)
type_ (src.features.smarterdb.Dataset attribute)
(src.features.smarterdb.SampleSpecies attribute)
U
UNKNOWN (src.features.smarterdb.SEX attribute)
UnknownCountry (class in src.features.utils)
update_affymetrix_record() (in module src.data.common)
update_chip_name() (in module src.data.common)
update_location() (in module src.data.common)
update_mapfile() (src.features.plinkio.SmarterMixin method)
update_pedfile() (src.features.plinkio.SmarterMixin method)
update_probesets() (in module src.data.common)
update_rs_id() (in module src.data.common)
update_sequence() (in module src.data.common)
update_variant() (in module src.data.common)
uploader (src.features.smarterdb.Dataset attribute)
V
VariantGoat (class in src.features.smarterdb)
VariantGoat.DoesNotExist
VariantGoat.MultipleObjectsReturned
variants_name (src.features.plinkio.SmarterMixin attribute)
VariantSheep (class in src.features.smarterdb)
VariantSheep.DoesNotExist
VariantSheep.MultipleObjectsReturned
VariantSpecies (class in src.features.smarterdb)
(src.features.plinkio.SmarterMixin attribute)
version (src.data.common.AssemblyConf attribute)
(src.features.smarterdb.Location attribute)
(src.features.smarterdb.SmarterInfo attribute)
W
warn_missing_cols (src.features.plinkio.AffyReportIO attribute)
working_assemblies (src.features.smarterdb.SmarterInfo attribute)
working_dir (src.features.smarterdb.Dataset property)
write() (src.features.utils.TqdmToLogger method)
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