Index

_

__init__() (genomfart.parsers.AGPmap.AGPMap method) (genomfart.parsers.SNPdata.SNPdata method) (genomfart.parsers.gff.gff_parser method) (genomfart.parsers.vcf.VCF_parser method) (genomfart.stats.pgm.Messenger method) (genomfart.stats.pgm.bayes_net method) (genomfart.stats.pgm.cpd method) (genomfart.stats.pgm.discrete_cpd method) (genomfart.stats.pgm.discrete_factor_graph method) (genomfart.utils.bigDataFrame.BigDataFrame method) (genomfart.utils.caching.LRUcache method) (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) (genomfart.utils.snp_projector.snp_projector method) (genomfart.utils.version_mapper.version_mapper method)

A

add_annotation() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) add_factor_node() (genomfart.stats.pgm.discrete_factor_graph method) add_node() (genomfart.stats.pgm.bayes_net method)

add_node_annotations() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) AGPMap (class in genomfart.parsers.AGPmap)

B

bayes_net (class in genomfart.stats.pgm) BigDataFrame (class in genomfart.utils.bigDataFrame)

bigDataFrameTest (class in genomfart.test.utils.bigDataFrameTest)

C

convert_to_discrete_factor_graph() (genomfart.stats.pgm.bayes_net method)

cpd (class in genomfart.stats.pgm)

D

discrete_cpd (class in genomfart.stats.pgm)

discrete_factor_graph (class in genomfart.stats.pgm)

F

findTotalSnpNumber() (genomfart.parsers.SNPdata.SNPdata method)

G

genetic_relationship (class in genomfart.popgen.genetic_relationship) genomeAnnotationGraph (class in genomfart.utils.genomeAnnotationGraph) genomfart (module) genomfart.data (module) genomfart.data.data_constants (module) genomfart.parsers (module) genomfart.parsers.AGPmap (module) genomfart.parsers.gff (module) genomfart.parsers.SNPdata (module) genomfart.parsers.vcf (module) genomfart.popgen (module) genomfart.popgen.genetic_relationship (module) genomfart.stats (module) genomfart.stats.pgm (module) genomfart.test (module) genomfart.test.parsers (module) genomfart.test.parsers.gffTest (module) genomfart.test.parsers.vcfTest (module) genomfart.test.utils (module) genomfart.test.utils.bigDataFrameTest (module) genomfart.test.utils.version_mapper_test (module) genomfart.utils (module) genomfart.utils.bigDataFrame (module) genomfart.utils.caching (module) genomfart.utils.genomeAnnotationGraph (module) genomfart.utils.polymorphism_formatter (module) genomfart.utils.scripts (module) genomfart.utils.scripts.shuffle_plink_phenotype_within_family (module) genomfart.utils.snp_projector (module) genomfart.utils.version_mapper (module) get_aa_indices() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_affected_ref_bases() (genomfart.parsers.vcf.VCF_parser static method) get_cds_indices() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_closest_element_id() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_closest_element_id_of_type() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_codon_position() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method)

get_current_row_ind() (genomfart.utils.bigDataFrame.BigDataFrame method) get_element_children_ids() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_element_ids_of_type() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_element_info() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_element_parent_ids() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_genetic_relationships() (genomfart.popgen.genetic_relationship.genetic_relationship static method) get_genetic_relationships_with_missing() (genomfart.popgen.genetic_relationship.genetic_relationship static method) get_genetic_relationships_with_missing_Endelman() (genomfart.popgen.genetic_relationship.genetic_relationship static method) get_name() (genomfart.stats.pgm.cpd method) get_norm_beliefs() (genomfart.stats.pgm.discrete_factor_graph method) get_nw_aligned_alleles() (genomfart.parsers.vcf.VCF_parser static method) get_overlapping_element_ids() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_overlapping_element_ids_of_type() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method) get_parents() (genomfart.stats.pgm.cpd method) get_prob() (genomfart.stats.pgm.discrete_cpd method) get_random_spanning_tree() (genomfart.stats.pgm.discrete_factor_graph method) get_substituted_ref_bases() (genomfart.parsers.vcf.VCF_parser static method) get_substituted_ref_bases_nw() (genomfart.parsers.vcf.VCF_parser static method) getAllele() (genomfart.parsers.SNPdata.SNPdata method) getCmFromPosition() (genomfart.parsers.AGPmap.AGPMap method) getFirstGeneticPosition() (genomfart.parsers.AGPmap.AGPMap method) getFirstMarkerName() (genomfart.parsers.AGPmap.AGPMap method) getFlankingMarkerIndices() (genomfart.parsers.AGPmap.AGPMap method) getGeneticPos() (genomfart.parsers.AGPmap.AGPMap method) getGenotype() (genomfart.parsers.SNPdata.SNPdata method) getInterval() (genomfart.parsers.AGPmap.AGPMap method) getLastGeneticPosition() (genomfart.parsers.AGPmap.AGPMap method) getLastMarkerName() (genomfart.parsers.AGPmap.AGPMap method) getMarkerNumber() (genomfart.parsers.AGPmap.AGPMap method) getNumberOfSnps() (genomfart.parsers.SNPdata.SNPdata method) getPhysPos() (genomfart.parsers.AGPmap.AGPMap method) getPosition() (genomfart.parsers.SNPdata.SNPdata method) getPositionFromCm() (genomfart.parsers.AGPmap.AGPMap method) gff_parser (class in genomfart.parsers.gff) gff_parserTest (class in genomfart.test.parsers.gffTest) graph (genomfart.utils.version_mapper.version_mapper attribute)

I

importMarkersForMap() (genomfart.utils.snp_projector.snp_projector method)

iterrows() (genomfart.utils.bigDataFrame.BigDataFrame method)

L

LRUcache (class in genomfart.utils.caching)

M

main() (in module genomfart.utils.scripts.shuffle_plink_phenotype_within_family) make_numpy_array() (genomfart.utils.bigDataFrame.BigDataFrame method)

Messenger (class in genomfart.stats.pgm)

N

next() (genomfart.parsers.SNPdata.SNPdata method)

O

overlaps_type() (genomfart.utils.genomeAnnotationGraph.genomeAnnotationGraph method)

P

parse_geno_depths() (genomfart.parsers.vcf.VCF_parser method) parse_select_geno_depths() (genomfart.parsers.vcf.VCF_parser method) parse_select_geno_generic() (genomfart.parsers.vcf.VCF_parser method) parse_site_infos() (genomfart.parsers.vcf.VCF_parser method)

plink (class in genomfart.utils.polymorphism_formatter) projectAllSnps() (genomfart.utils.snp_projector.snp_projector method) projectSnpBoolean() (genomfart.utils.snp_projector.snp_projector method)

R

reset() (genomfart.parsers.SNPdata.SNPdata method) reset_nonobs_messages() (genomfart.stats.pgm.discrete_factor_graph method) run_BP_tree() (genomfart.stats.pgm.discrete_factor_graph method)

run_synchronous_LBP() (genomfart.stats.pgm.discrete_factor_graph method) run_synchronous_update() (genomfart.stats.pgm.discrete_factor_graph method)

S

send_message_to_factor() (genomfart.stats.pgm.discrete_factor_graph method) send_message_to_var() (genomfart.stats.pgm.discrete_factor_graph method) set_variable_state() (genomfart.stats.pgm.discrete_factor_graph method) set_variable_unobserved() (genomfart.stats.pgm.discrete_factor_graph method)

setUpClass() (genomfart.test.parsers.gffTest.gff_parserTest class method) (genomfart.test.parsers.vcfTest.vcfTest class method) (genomfart.test.utils.bigDataFrameTest.bigDataFrameTest class method) (genomfart.test.utils.version_mapper_test.version_mapper_test class method) shuffle_pheno_within_family() (in module genomfart.utils.scripts.shuffle_plink_phenotype_within_family) snp_projector (class in genomfart.utils.snp_projector) SNPdata (class in genomfart.parsers.SNPdata)

T

test_get_aa_indices() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_affected_ref_bases() (genomfart.test.parsers.vcfTest.vcfTest method) test_get_cds_indices() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_closest_element_id() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_closest_element_id_of_type() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_codon_position() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_element_children_ids() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_element_ids_of_type() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_element_info() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_element_parent_ids() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_nw_aligned_alleles() (genomfart.test.parsers.vcfTest.vcfTest method) test_get_overlapping_element_ids() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_overlapping_element_ids_of_type() (genomfart.test.parsers.gffTest.gff_parserTest method) test_get_substituted_ref_bases() (genomfart.test.parsers.vcfTest.vcfTest method)

test_get_substituted_ref_bases_nw() (genomfart.test.parsers.vcfTest.vcfTest method) test_getitem() (genomfart.test.utils.bigDataFrameTest.bigDataFrameTest method) test_iter() (genomfart.test.utils.bigDataFrameTest.bigDataFrameTest method) test_iterrow() (genomfart.test.utils.bigDataFrameTest.bigDataFrameTest method) test_make_numpy_array() (genomfart.test.utils.bigDataFrameTest.bigDataFrameTest method) test_overlaps_type() (genomfart.test.parsers.gffTest.gff_parserTest method) test_parse_geno_depths() (genomfart.test.parsers.vcfTest.vcfTest method) test_parse_select_geno_depths() (genomfart.test.parsers.vcfTest.vcfTest method) test_parse_select_geno_generic() (genomfart.test.parsers.vcfTest.vcfTest method) test_parse_site_infos() (genomfart.test.parsers.vcfTest.vcfTest method) test_v1_to_v2_map() (genomfart.test.utils.version_mapper_test.version_mapper_test method) test_v1_to_v2_seg_map() (genomfart.test.utils.version_mapper_test.version_mapper_test method) test_v2_to_v1_map() (genomfart.test.utils.version_mapper_test.version_mapper_test method) test_v2_to_v1_seg_map() (genomfart.test.utils.version_mapper_test.version_mapper_test method)

V

v1_end_dict (genomfart.utils.version_mapper.version_mapper attribute) v1_to_v2_map() (genomfart.utils.version_mapper.version_mapper method) v1_to_v2_seg_map() (genomfart.utils.version_mapper.version_mapper method) v2_end_dict (genomfart.utils.version_mapper.version_mapper attribute) v2_to_v1_map() (genomfart.utils.version_mapper.version_mapper method)

v2_to_v1_seg_map() (genomfart.utils.version_mapper.version_mapper method) VCF_parser (class in genomfart.parsers.vcf) vcfTest (class in genomfart.test.parsers.vcfTest) version_mapper (class in genomfart.utils.version_mapper) version_mapper_test (class in genomfart.test.utils.version_mapper_test)

W

write_geno_mat_to_ped() (genomfart.utils.polymorphism_formatter.plink static method) write_libpgm_file() (genomfart.stats.pgm.bayes_net method)

write_libpgm_json() (in module genomfart.stats.pgm)