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) add_r_lib() (in module pygtftk.utils) as_data_frame() (pygtftk.tab_interface.TAB method) as_dict() (pygtftk.fasta_interface.FASTA method) as_simple_list() (pygtftk.tab_interface.TAB method)

B

bw_cov_mp() (in module pygtftk.bwig.bw_coverage)

bw_profile_mp() (in module pygtftk.bwig.bw_coverage)

C

check_file_or_dir_exists() (in module pygtftk.utils) 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) convert_to_ensembl() (pygtftk.gtf_interface.GTF method)

D

del_attr() (pygtftk.gtf_interface.GTF method)

E

enumerate() (pygtftk.fasta_interface.FASTA 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) 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

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_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_intergenic() (pygtftk.gtf_interface.GTF method) get_introns() (pygtftk.gtf_interface.GTF method) get_midpoints() (pygtftk.gtf_interface.GTF method) get_sequences() (pygtftk.gtf_interface.GTF 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

head() (pygtftk.gtf_interface.GTF method)

head_file() (in module pygtftk.utils)

I

intervals() (in module pygtftk.utils) is_comment() (in module pygtftk.utils) is_empty() (in module pygtftk.utils) is_exon() (in module pygtftk.utils)

is_fasta_header() (in module pygtftk.utils) iter_as_list() (pygtftk.tab_interface.TAB method) iter_features() (pygtftk.fasta_interface.FASTA method) iterate_with_header() (pygtftk.tab_interface.TAB method)

M

make_outdir_and_file() (in module pygtftk.utils) make_tmp_file() (in module pygtftk.utils) median_comp() (in module pygtftk.utils)

merge_attr() (pygtftk.gtf_interface.GTF method) message() (in module pygtftk.utils) mkdir_p() (in module pygtftk.utils)

N

nb_exons() (pygtftk.gtf_interface.GTF method)

nrow() (pygtftk.gtf_interface.GTF method)

P

pygtftk.bwig.bw_coverage (module) pygtftk.fasta_interface (module) pygtftk.gtf_interface (module)

pygtftk.Line (module) pygtftk.tab_interface (module) pygtftk.utils (module)

R

random_string() (in module pygtftk.utils)

S

select_5p_transcript() (pygtftk.gtf_interface.GTF 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_numeric_value() (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)

T

TAB (class in pygtftk.tab_interface) tab_line() (in module pygtftk.utils) tail() (pygtftk.gtf_interface.GTF method)

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

W

write() (pygtftk.fasta_interface.FASTA method) (pygtftk.Line.FastaSequence method) (pygtftk.Line.Feature method) (pygtftk.Line.FieldSet method) (pygtftk.gtf_interface.GTF method) (pygtftk.tab_interface.TAB method)

write_bed() (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)