Index

_

_gene_codes_and_lengths (dataset_creator.Dataset attribute), [1] (dataset_creator.dataset.Dataset attribute), [1]

A

add_suffixes_to_gene_codes() (dataset_creator.base_dataset.DatasetFooter method), [1]

B

BasePairCount (class in dataset_creator.base_dataset), [1]

C

convert_block_dicts_to_string() (dataset_creator.base_dataset.DatasetBlock method), [1] convert_blocks_to_string() (dataset_creator.mega.MegaDatasetBlock method), [1] convert_nexus_to_format() (in module dataset_creator.utils), [1] convert_to_string() (dataset_creator.base_dataset.DatasetBlock method), [1] (dataset_creator.genbank_fasta.GenBankFASTADatasetBlock method), [1] (dataset_creator.tnt.TntDatasetBlock method), [1] correct_count_using_reading_frames() (dataset_creator.base_dataset.DatasetFooter method), [1]

create_dataset_block() (dataset_creator.creator.Creator method), [1] create_dataset_footer() (dataset_creator.creator.Creator method), [1] create_dataset_header() (dataset_creator.creator.Creator method), [1] create_extra_dataset_file() (dataset_creator.creator.Creator method), [1] Creator (class in dataset_creator.creator), [1]

D

Dataset (class in dataset_creator), [1] (class in dataset_creator.dataset), [1] dataset_block() (dataset_creator.base_dataset.DatasetBlock method), [1] (dataset_creator.mega.MegaDatasetBlock method), [1] (dataset_creator.tnt.TntDatasetBlock method), [1] dataset_creator (module), [1] dataset_creator.base_dataset (module), [1] dataset_creator.creator (module), [1] dataset_creator.dataset (module), [1] dataset_creator.exceptions (module), [1] dataset_creator.genbank_fasta (module), [1]

dataset_creator.mega (module), [1] dataset_creator.phylip (module), [1] dataset_creator.tnt (module), [1] dataset_creator.utils (module), [1] dataset_footer() (dataset_creator.base_dataset.DatasetFooter method), [1] DatasetBlock (class in dataset_creator.base_dataset), [1] DatasetFooter (class in dataset_creator.base_dataset), [1]

E

extra_dataset_str (dataset_creator.creator.Creator attribute), [1]

F

flatten_taxonomy() (dataset_creator.base_dataset.DatasetBlock method), [1]

format_charset_line() (dataset_creator.base_dataset.DatasetFooter method), [1]

G

GenBankFASTADatasetBlock (class in dataset_creator.genbank_fasta), [1] get_corrected_count() (dataset_creator.base_dataset.BasePairCount method), [1]

get_outgroup() (dataset_creator.base_dataset.DatasetFooter method), [1] get_seq() (in module dataset_creator.utils), [1]

M

make_charset_block() (dataset_creator.base_dataset.DatasetFooter method), [1] (dataset_creator.phylip.PhylipDatasetFooter method), [1] make_charsets() (dataset_creator.base_dataset.DatasetFooter method), [1] (dataset_creator.phylip.PhylipDatasetFooter method), [1] make_datablock_by_gene() (dataset_creator.base_dataset.DatasetBlock method), [1] make_datablock_considering_codon_positions_as_fasta_format() (dataset_creator.base_dataset.DatasetBlock method), [1] make_dataset_header() (in module dataset_creator.utils), [1] make_footer() (dataset_creator.base_dataset.DatasetFooter method), [1]

make_gene_code_suffixes() (dataset_creator.base_dataset.DatasetFooter method), [1] make_partition_line() (dataset_creator.base_dataset.DatasetFooter method), [1] make_random_filename() (in module dataset_creator.utils), [1] make_slash_number() (dataset_creator.base_dataset.DatasetFooter method), [1] MegaDatasetBlock (class in dataset_creator.mega), [1]

P

PhylipDatasetFooter (class in dataset_creator.phylip), [1] put_everything_together() (dataset_creator.creator.Creator method), [1]

put_outgroup_at_start_of_block() (dataset_creator.tnt.TntDatasetBlock method), [1]

R

read_and_delete_tmp_file() (in module dataset_creator.utils), [1]

S

sort_seq_records() (dataset_creator.Dataset method), [1] (dataset_creator.dataset.Dataset method), [1] split_data() (dataset_creator.base_dataset.DatasetBlock method), [1]

suffix_for_one_codon_position() (dataset_creator.base_dataset.DatasetFooter method), [1] suffix_for_several_codon_positions() (dataset_creator.base_dataset.DatasetFooter method), [1]

T

TntDatasetBlock (class in dataset_creator.tnt), [1]

W

WrongParameterFormat, [1]