Index

A

add_attr() (pygtftk.Line.Feature method) add_attr_and_write() (pygtftk.Line.Feature method) add_attr_column() (pygtftk.gtf_interface.GTF method) add_attr_from_dict() (pygtftk.gtf_interface.GTF method) add_attr_from_file() (pygtftk.gtf_interface.GTF method) add_attr_from_list() (pygtftk.gtf_interface.GTF method) add_attr_from_matrix_file() (pygtftk.gtf_interface.GTF method)

add_attr_to_pos() (pygtftk.gtf_interface.GTF method) add_exon_number() (pygtftk.gtf_interface.GTF method) add_prefix() (pygtftk.gtf_interface.GTF method) add_prefix_to_file() (in module pygtftk.utils) apply_recursively_to_all_nodes() (in module pygtftk.stats.intersect.modl.tree) as_data_frame() (pygtftk.tab_interface.TAB method) as_simple_list() (pygtftk.tab_interface.TAB method)

B

beta() (pygtftk.stats.beta.BetaCalculator method) beta_pval() (in module pygtftk.stats.beta) BetaCalculator (class in pygtftk.stats.beta) betainc() (pygtftk.stats.beta.BetaCalculator method) betaincreg() (pygtftk.stats.beta.BetaCalculator method)

build_best_dict_from_library() (in module pygtftk.stats.intersect.modl.subroutines) build_nodes_for_words() (pygtftk.stats.intersect.modl.tree.Library method) build_nodes_for_words_from_ologram_result_df() (pygtftk.stats.intersect.modl.tree.Library method) bw_cov_mp() (in module pygtftk.bwig.bw_coverage) bw_profile_mp() (in module pygtftk.bwig.bw_coverage)

C

check_boolean_exprs() (in module pygtftk.utils) check_file_or_dir_exists() (in module pygtftk.utils) check_negbin_adjustment() (in module pygtftk.stats.negbin_fit) check_r_installed() (in module pygtftk.utils) check_r_packages() (in module pygtftk.utils) chomp() (in module pygtftk.utils) chrom_info_as_dict() (in module pygtftk.utils) chrom_info_to_bed_file() (in module pygtftk.utils) close_properly() (in module pygtftk.utils)

CombinationExactMapping (class in pygtftk.stats.intersect.overlap_stats_compute) compute_all_intersections_minibatch() (in module pygtftk.stats.intersect.overlap_stats_shuffling) compute_overlap_stats() (in module pygtftk.stats.intersect.overlap_stats_shuffling) compute_stats_for_intersection() (in module pygtftk.stats.intersect.overlap_stats_compute) compute_true_intersection() (in module pygtftk.stats.intersect.overlap_stats_compute) ComputingIntersectionPartial (class in pygtftk.stats.intersect.overlap_stats_shuffling) contfractbeta() (pygtftk.stats.beta.BetaCalculator method) convert_to_ensembl() (pygtftk.gtf_interface.GTF method) Counter (class in pygtftk.stats.intersect.overlap_stats_compute)

D

del_attr() (pygtftk.gtf_interface.GTF method)

DictionaryWithIndex (class in pygtftk.stats.intersect.overlap_stats_compute)

E

empirical_p_val() (in module pygtftk.stats.negbin_fit) eval_numeric() (pygtftk.gtf_interface.GTF method)

extract_data() (pygtftk.gtf_interface.GTF method) extract_data_iter_list() (pygtftk.gtf_interface.GTF method)

F

FASTA (class in pygtftk.fasta_interface) FastaSequence (class in pygtftk.Line) Feature (class in pygtftk.Line) FieldSet (class in pygtftk.Line) find_interesting_combinations() (pygtftk.stats.intersect.modl.dict_learning.Modl method) fit_beta() (in module pygtftk.stats.beta)

flatten_list() (in module pygtftk.utils) flatten_list_recur() (in module pygtftk.utils) format() (pygtftk.Line.FastaSequence method) (pygtftk.Line.Feature method) (pygtftk.Line.FieldSet method) format_tab() (pygtftk.Line.Feature method) from_list() (pygtftk.Line.Feature class method)

G

generate_candidate_words() (in module pygtftk.stats.intersect.modl.subroutines) (pygtftk.stats.intersect.modl.dict_learning.Modl method) get_3p_end() (pygtftk.gtf_interface.GTF method) (pygtftk.Line.Feature method) get_5p_end() (pygtftk.gtf_interface.GTF method) (pygtftk.Line.Feature method) get_all_candidates_except() (in module pygtftk.stats.intersect.modl.tree) get_attr_list() (pygtftk.gtf_interface.GTF method) get_attr_names() (pygtftk.Line.Feature method) get_attr_value() (pygtftk.Line.Feature method) get_attr_value_list() (pygtftk.gtf_interface.GTF method) get_chroms() (pygtftk.gtf_interface.GTF method) get_example_feature() (in module pygtftk.utils) get_example_file() (in module pygtftk.utils) get_feature_list() (pygtftk.gtf_interface.GTF method) get_feature_size() (pygtftk.gtf_interface.GTF method) get_gn_id() (pygtftk.Line.Feature method) get_gn_ids() (pygtftk.gtf_interface.GTF method) get_gn_strand() (pygtftk.gtf_interface.GTF method)

get_gn_to_tx() (pygtftk.gtf_interface.GTF method) get_gname_to_tx() (pygtftk.gtf_interface.GTF method) get_index_if_present() (in module pygtftk.stats.intersect.overlap_stats_compute) get_intergenic() (pygtftk.gtf_interface.GTF method) get_introns() (pygtftk.gtf_interface.GTF method) get_items_by_indices_in_list() (in module pygtftk.stats.intersect.overlap_stats_compute) get_midpoints() (pygtftk.gtf_interface.GTF method) get_sequences() (pygtftk.gtf_interface.GTF method) get_simple_concatenation() (pygtftk.stats.intersect.overlap_stats_compute.DictionaryWithIndex method) get_transcript_size() (pygtftk.gtf_interface.GTF method) get_tss() (pygtftk.gtf_interface.GTF method) get_tts() (pygtftk.gtf_interface.GTF method) get_tx_id() (pygtftk.Line.Feature method) get_tx_ids() (pygtftk.gtf_interface.GTF method) get_tx_strand() (pygtftk.gtf_interface.GTF method) get_tx_to_gn() (pygtftk.gtf_interface.GTF method) get_tx_to_gname() (pygtftk.gtf_interface.GTF method) GTF (class in pygtftk.gtf_interface) GTFtkError GTFtkInteractiveError

H

HashableArray (class in pygtftk.stats.intersect.overlap_stats_compute)

head() (pygtftk.gtf_interface.GTF method) head_file() (in module pygtftk.utils)

I

index_all_these() (in module pygtftk.stats.intersect.overlap_stats_compute) intervals() (in module pygtftk.utils) is_comment() (in module pygtftk.utils) is_defined() (pygtftk.gtf_interface.GTF method) is_empty() (in module pygtftk.utils)

is_exon() (in module pygtftk.utils) is_fasta_header() (in module pygtftk.utils) is_set() (pygtftk.gtf_interface.GTF method) iter_as_list() (pygtftk.tab_interface.TAB method) iterate_with_header() (pygtftk.tab_interface.TAB method)

L

learn_dictionary_and_encode() (in module pygtftk.stats.intersect.modl.subroutines)

Library (class in pygtftk.stats.intersect.modl.tree)

M

make_outdir_and_file() (in module pygtftk.utils) make_tmp_dir() (in module pygtftk.utils) make_tmp_file() (in module pygtftk.utils) make_tmp_file_pool() (in module pygtftk.bwig.bw_coverage) median_comp() (in module pygtftk.utils) merge_attr() (pygtftk.gtf_interface.GTF method) merge_consecutive_intersections_in_all_overlaps_lists() (in module pygtftk.stats.intersect.overlap_stats_compute) merge_consecutive_intersections_in_intersections_list() (in module pygtftk.stats.intersect.overlap_stats_compute) message() (in module pygtftk.utils) (pygtftk.gtf_interface.GTF method) mkdir_p() (in module pygtftk.utils) Modl (class in pygtftk.stats.intersect.modl.dict_learning) module pygtftk.bwig.bw_coverage pygtftk.fasta_interface pygtftk.gtf_interface pygtftk.Line pygtftk.stats.beta pygtftk.stats.intersect.modl.dict_learning pygtftk.stats.intersect.modl.subroutines pygtftk.stats.intersect.modl.tree pygtftk.stats.intersect.overlap_stats_compute pygtftk.stats.intersect.overlap_stats_shuffling pygtftk.stats.negbin_fit pygtftk.tab_interface pygtftk.utils

N

nb_exons() (pygtftk.gtf_interface.GTF method) negbin_pval() (in module pygtftk.stats.negbin_fit) nested_dict() (in module pygtftk.utils)

Node (class in pygtftk.stats.intersect.modl.tree) normalize_and_jitter_matrix_rows() (in module pygtftk.stats.intersect.modl.subroutines) nrow() (pygtftk.gtf_interface.GTF method)

O

output_visualize() (in module pygtftk.stats.intersect.modl.tree)

P

put() (pygtftk.stats.intersect.overlap_stats_compute.SparseListOfLists method) pygtftk.bwig.bw_coverage module pygtftk.fasta_interface module pygtftk.gtf_interface module pygtftk.Line module pygtftk.stats.beta module pygtftk.stats.intersect.modl.dict_learning module

pygtftk.stats.intersect.modl.subroutines module pygtftk.stats.intersect.modl.tree module pygtftk.stats.intersect.overlap_stats_compute module pygtftk.stats.intersect.overlap_stats_shuffling module pygtftk.stats.negbin_fit module pygtftk.tab_interface module pygtftk.utils module

R

random_string() (in module pygtftk.utils)

rnd_alpha_numeric_string() (in module pygtftk.utils)

S

select_5p_transcript() (pygtftk.gtf_interface.GTF method) select_best_words_from_library() (pygtftk.stats.intersect.modl.dict_learning.Modl method) select_by_key() (pygtftk.gtf_interface.GTF method) select_by_loc() (pygtftk.gtf_interface.GTF method) select_by_max_exon_nb() (pygtftk.gtf_interface.GTF method) select_by_number_of_exons() (pygtftk.gtf_interface.GTF method) select_by_positions() (pygtftk.gtf_interface.GTF method) select_by_regexp() (pygtftk.gtf_interface.GTF method) select_by_transcript_size() (pygtftk.gtf_interface.GTF method) select_longuest_transcripts() (pygtftk.gtf_interface.GTF method)

select_shortest_transcripts() (pygtftk.gtf_interface.GTF method) set_attr() (pygtftk.Line.Feature method) silentremove() (in module pygtftk.utils) simple_line_count() (in module pygtftk.utils) simple_nb_column() (in module pygtftk.utils) sort_2_lists() (in module pygtftk.utils) SparseListOfLists (class in pygtftk.stats.intersect.overlap_stats_compute) squish_matrix() (in module pygtftk.stats.intersect.modl.dict_learning) stats_multiple_overlap() (in module pygtftk.stats.intersect.overlap_stats_compute) stats_single() (in module pygtftk.stats.intersect.overlap_stats_compute)

T

TAB (class in pygtftk.tab_interface) tab_line() (in module pygtftk.utils) tail() (pygtftk.gtf_interface.GTF method) test_data_for_modl() (in module pygtftk.stats.intersect.modl.dict_learning)

to_alphanum() (in module pygtftk.utils) to_bed() (pygtftk.gtf_interface.GTF method) to_list() (in module pygtftk.utils) transcript_as_bioseq_records() (pygtftk.fasta_interface.FASTA method)

W

which_combis_to_get_from() (in module pygtftk.stats.intersect.overlap_stats_compute) write() (pygtftk.fasta_interface.FASTA method) (pygtftk.gtf_interface.GTF method) (pygtftk.Line.FastaSequence method) (pygtftk.Line.Feature method) (pygtftk.Line.FieldSet method) (pygtftk.tab_interface.TAB method)

write_bed() (pygtftk.gtf_interface.GTF method) (pygtftk.Line.Feature method) write_bed_3p_end() (pygtftk.Line.Feature method) write_bed_5p_end() (pygtftk.Line.Feature method) write_gtf_to_bed6() (pygtftk.Line.Feature method) write_properly() (in module pygtftk.utils)