Index

A

ases_df() (in module aspring.step_08_ASRUs) aspring module aspring.main module aspring.step_01_preprocess module aspring.step_02_hmm_maker module aspring.step_03_hmm_aligner module aspring.step_04_gettable module

aspring.step_05_filter module aspring.step_06_stats module aspring.step_07_reformat module aspring.step_08_ASRUs module aspring.step_09_clean module aspring.step_10_struct module

C

check_if_executable_exists() (in module aspring.main)

codage() (in module aspring.step_08_ASRUs)

D

download_alphafold_structure() (in module aspring.step_10_struct)

download_pdb_structures() (in module aspring.step_10_struct) dupraw2table() (in module aspring.step_04_gettable)

E

event_to_pairs() (in module aspring.step_08_ASRUs) eventsDup_df() (in module aspring.step_08_ASRUs)

extension_marge_pair() (in module aspring.step_08_ASRUs) extensionbis() (in module aspring.step_08_ASRUs)

F

filter() (in module aspring.step_05_filter)

G

get_alnCols() (in module aspring.step_08_ASRUs) get_arg_parser() (in module aspring.main) (in module aspring.step_01_preprocess) (in module aspring.step_02_hmm_maker) (in module aspring.step_03_hmm_aligner) (in module aspring.step_04_gettable) (in module aspring.step_05_filter) (in module aspring.step_06_stats) (in module aspring.step_07_reformat) (in module aspring.step_08_ASRUs) (in module aspring.step_09_clean) (in module aspring.step_10_struct)

get_asrus() (in module aspring.step_10_struct) get_pdb_sequence_length() (in module aspring.step_10_struct) get_pdb_span() (in module aspring.step_10_struct) get_sexon_coord() (in module aspring.step_10_struct) get_sexon_id() (in module aspring.step_10_struct) get_transcript_sequence_length() (in module aspring.step_10_struct) get_transcripts() (in module aspring.step_10_struct) get_uniprot_id_from_filename() (in module aspring.step_10_struct) get_uniprot_ids() (in module aspring.step_10_struct)

H

hhr2df() (in module aspring.step_04_gettable)

hmm_aligner() (in module aspring.step_03_hmm_aligner) hmm_maker() (in module aspring.step_02_hmm_maker)

M

module aspring aspring.main aspring.step_01_preprocess aspring.step_02_hmm_maker aspring.step_03_hmm_aligner aspring.step_04_gettable aspring.step_05_filter aspring.step_06_stats aspring.step_07_reformat aspring.step_08_ASRUs aspring.step_09_clean aspring.step_10_struct

P

parse_args() (in module aspring.main) (in module aspring.step_01_preprocess) (in module aspring.step_02_hmm_maker) (in module aspring.step_03_hmm_aligner) (in module aspring.step_04_gettable) (in module aspring.step_05_filter) (in module aspring.step_06_stats) (in module aspring.step_07_reformat) (in module aspring.step_08_ASRUs) (in module aspring.step_09_clean) (in module aspring.step_10_struct)

preprocess_msas() (in module aspring.step_01_preprocess)

R

read_fasta() (in module aspring.step_04_gettable) reformate() (in module aspring.step_07_reformat) rm_tempfiles() (in module aspring.step_09_clean) run() (in module aspring.main) (in module aspring.step_01_preprocess) (in module aspring.step_02_hmm_maker) (in module aspring.step_03_hmm_aligner) (in module aspring.step_04_gettable) (in module aspring.step_05_filter) (in module aspring.step_06_stats) (in module aspring.step_07_reformat) (in module aspring.step_08_ASRUs) (in module aspring.step_09_clean) (in module aspring.step_10_struct)

run_pipeline() (in module aspring.main) run_r_script() (in module aspring.step_06_stats)

S

sexSize() (in module aspring.step_08_ASRUs) sim_graph_initial() (in module aspring.step_08_ASRUs)

sim_graph_initial_bis() (in module aspring.step_08_ASRUs) sim_graph_workframe() (in module aspring.step_08_ASRUs)

T

test_rscript_availability() (in module aspring.step_06_stats)

W

write_pml() (in module aspring.step_10_struct)

writecsv_ASRU() (in module aspring.step_08_ASRUs)