Index

Symbols

--download-example-data proksee-batch command line option --input proksee-batch command line option

--output proksee-batch command line option --version proksee-batch command line option

A

add_bed_features_and_tracks() (in module proksee_batch.parse_additional_features) add_blast_features_and_tracks() (in module proksee_batch.parse_additional_features)

add_gff_features_and_tracks() (in module proksee_batch.parse_additional_features) add_vcf_features_and_tracks() (in module proksee_batch.parse_additional_features)

B

BedFeatureDict (class in proksee_batch.parse_additional_features) BedMetaDict (class in proksee_batch.parse_additional_features)

BlastFeatureDict (class in proksee_batch.parse_additional_features) BlastMetaDict (class in proksee_batch.parse_additional_features)

C

check_vcf_ref_vs_alt_genotypes() (in module proksee_batch.validate_input_data)

check_vcf_seq_ids() (in module proksee_batch.validate_input_data)

D

download_example_genbank_files() (in module proksee_batch.download_example_input) download_example_input() (in module proksee_batch.download_example_input)

download_file() (in module proksee_batch.download_example_input) download_genbank_file() (in module proksee_batch.download_example_input)

F

fasta_to_cgview_json() (in module proksee_batch.seq_file_to_cgview_json)

FeatureDecorationDict (class in proksee_batch.parse_additional_features)

G

genbank_to_cgview_json() (in module proksee_batch.seq_file_to_cgview_json) generate_js_data() (in module proksee_batch.__main__) generate_report_html() (in module proksee_batch.generate_report_html) get_data_files() (in module proksee_batch.validate_input_data) get_description_from_metadata() (in module proksee_batch.__main__) get_feature_locations_and_scores_from_bed_features() (in module proksee_batch.parse_additional_features)

get_feature_locations_and_scores_from_blast_features() (in module proksee_batch.parse_additional_features) get_feature_locations_and_scores_from_gff_features() (in module proksee_batch.parse_additional_features) get_feature_locations_and_scores_from_vcf_features() (in module proksee_batch.parse_additional_features) get_stats_from_seq_file() (in module proksee_batch.get_stats_from_seq_file) GffFeatureDict (class in proksee_batch.parse_additional_features) GffMetaDict (class in proksee_batch.parse_additional_features)

H

handle_error_exit() (in module proksee_batch.__main__) (in module proksee_batch.validate_input_data)

M

merge_cgview_json_with_template() (in module proksee_batch.merge_cgview_json_with_template) module proksee_batch proksee_batch.__main__ proksee_batch.download_example_input proksee_batch.generate_report_html proksee_batch.get_stats_from_seq_file proksee_batch.merge_cgview_json_with_template proksee_batch.parse_additional_features proksee_batch.seq_file_to_cgview_json proksee_batch.validate_input_data

P

parse_bed_files() (in module proksee_batch.parse_additional_features) parse_blast_files() (in module proksee_batch.parse_additional_features) parse_gff_files() (in module proksee_batch.parse_additional_features) parse_vcf_files() (in module proksee_batch.parse_additional_features) proksee-batch command line option --download-example-data --input --output --version proksee_batch module proksee_batch.__main__ module

proksee_batch.download_example_input module proksee_batch.generate_report_html module proksee_batch.get_stats_from_seq_file module proksee_batch.merge_cgview_json_with_template module proksee_batch.parse_additional_features module proksee_batch.seq_file_to_cgview_json module proksee_batch.validate_input_data module

R

remove_problematic_characters_from_contig_name() (in module proksee_batch.seq_file_to_cgview_json)

S

seq_to_json_contig() (in module proksee_batch.seq_file_to_cgview_json)

T

TrackDict (class in proksee_batch.parse_additional_features)

V

validate_input_directory_contents() (in module proksee_batch.validate_input_data)

VcfFeatureDict (class in proksee_batch.parse_additional_features) VcfMetaDict (class in proksee_batch.parse_additional_features)