Index

_

__init__() (snps.ensembl.EnsemblRestClient method) (snps.io.reader.Reader method) (snps.io.writer.Writer method) (snps.resources.ReferenceSequence method) (snps.resources.Resources method) (snps.snps.SNPs method) (snps.utils.Parallelizer method)

A

assembly (snps.resources.ReferenceSequence property) (snps.snps.SNPs property)

B

build (snps.resources.ReferenceSequence property) (snps.snps.SNPs property)

build_detected (snps.snps.SNPs property)

C

chip (snps.snps.SNPs property) chip_version (snps.snps.SNPs property) chrom (snps.resources.ReferenceSequence property) chromosomes (snps.snps.SNPs property) chromosomes_summary (snps.snps.SNPs property)

clean_str() (in module snps.utils) clear() (snps.resources.ReferenceSequence method) cluster (snps.snps.SNPs property) compute_cluster_overlap() (snps.snps.SNPs method) count (snps.snps.SNPs property) create_dir() (in module snps.utils)

D

detect_build() (snps.snps.SNPs method) determine_sex() (snps.snps.SNPs method) discrepant_merge_genotypes (snps.snps.SNPs property) discrepant_merge_positions (snps.snps.SNPs property)

discrepant_merge_positions_genotypes (snps.snps.SNPs property) discrepant_vcf_position (snps.snps.SNPs property) discrepant_XY (snps.snps.SNPs property) download_example_datasets() (snps.resources.Resources method) duplicate (snps.snps.SNPs property)

E

end (snps.resources.ReferenceSequence property)

EnsemblRestClient (class in snps.ensembl)

G

get_all_reference_sequences() (snps.resources.Resources method) get_all_resources() (snps.resources.Resources method) get_assembly_mapping_data() (snps.resources.Resources method) get_chip_clusters() (snps.resources.Resources method) get_count() (snps.snps.SNPs method) get_dbsnp_151_37_reverse() (snps.resources.Resources method) get_empty_snps_dataframe() (in module snps.io.reader)

get_gsa_chrpos() (snps.resources.Resources method) get_gsa_resources() (snps.resources.Resources method) get_gsa_rsid() (snps.resources.Resources method) get_low_quality_snps() (snps.resources.Resources method) get_opensnp_datadump_filenames() (snps.resources.Resources method) get_par_regions() (snps.snps.SNPs static method) get_reference_sequences() (snps.resources.Resources method) gzip_file() (in module snps.utils)

H

heterozygous() (snps.snps.SNPs method)

heterozygous_MT (snps.snps.SNPs property) homozygous() (snps.snps.SNPs method)

I

ID (snps.resources.ReferenceSequence property) identify_low_quality_snps() (snps.snps.SNPs method)

is_gzip() (snps.io.reader.Reader static method) is_zip() (snps.io.reader.Reader static method)

L

length (snps.resources.ReferenceSequence property)

load_opensnp_datadump_file() (snps.resources.Resources method) low_quality (snps.snps.SNPs property)

M

md5 (snps.resources.ReferenceSequence property) merge() (snps.snps.SNPs method) module snps.ensembl snps.io snps.io.reader snps.io.writer snps.resources snps.snps snps.utils

N

notnull() (snps.snps.SNPs method)

P

Parallelizer (class in snps.utils) path (snps.resources.ReferenceSequence property)

perform_rest_action() (snps.ensembl.EnsemblRestClient method) phased (snps.snps.SNPs property) predict_ancestry() (snps.snps.SNPs method)

R

read() (snps.io.reader.Reader method) read_23andme() (snps.io.reader.Reader method) read_ancestry() (snps.io.reader.Reader method) read_circledna() (snps.io.reader.Reader method) read_dnaland() (snps.io.reader.Reader method) read_ftdna() (snps.io.reader.Reader method) read_ftdna_famfinder() (snps.io.reader.Reader method) read_generic() (snps.io.reader.Reader method) read_genes_for_good() (snps.io.reader.Reader method) read_gsa() (snps.io.reader.Reader method)

read_helper() (snps.io.reader.Reader method) read_livingdna() (snps.io.reader.Reader method) read_mapmygenome() (snps.io.reader.Reader method) read_myheritage() (snps.io.reader.Reader method) read_snps_csv() (snps.io.reader.Reader method) read_tellmegen() (snps.io.reader.Reader method) read_vcf() (snps.io.reader.Reader method) Reader (class in snps.io.reader) ReferenceSequence (class in snps.resources) remap() (snps.snps.SNPs method) Resources (class in snps.resources)

S

save_df_as_csv() (in module snps.utils) sequence (snps.resources.ReferenceSequence property) sex (snps.snps.SNPs property) Singleton (class in snps.utils) SNPs (class in snps.snps) snps (snps.snps.SNPs property) snps.ensembl module snps.io module snps.io.reader module snps.io.writer module

snps.resources module snps.snps module snps.utils module snps_qc (snps.snps.SNPs property) sort() (snps.snps.SNPs method) source (snps.snps.SNPs property) species (snps.resources.ReferenceSequence property) start (snps.resources.ReferenceSequence property) summary (snps.snps.SNPs property)

T

taxonomy (snps.resources.ReferenceSequence property) to_csv() (snps.snps.SNPs method)

to_tsv() (snps.snps.SNPs method) to_vcf() (snps.snps.SNPs method)

U

unannotated_vcf (snps.snps.SNPs property)

url (snps.resources.ReferenceSequence property)

V

valid (snps.snps.SNPs property)

W

write() (snps.io.writer.Writer method)

Writer (class in snps.io.writer)

Z

zip_file() (in module snps.utils)