aspring package

Submodules

aspring.main module

aspring.main.check_if_executable_exists(executable)

aspring.main.get_arg_parser()

aspring.main.parse_args(args)

aspring.main.run()

aspring.main.run_pipeline(gene, path_data, path_hhsuite_scripts, msa_len, msa_id_threshold, re_align, glo_loc, mact, id_pair, idCons_pair, pval, nbSpe, cov)

aspring.step_01_preprocess module

aspring.step_01_preprocess.get_arg_parser()

aspring.step_01_preprocess.parse_args(args)

aspring.step_01_preprocess.preprocess_msas(gene, path_data, path_hhsuite, msa_len)

aspring.step_01_preprocess.run()

Entry point for the application script

aspring.step_02_hmm_maker module

aspring.step_02_hmm_maker.get_arg_parser()

aspring.step_02_hmm_maker.hmm_maker(gene, msa_id_threshold, path_data)

Create HMM profiles for all s-exons of a chosen gene

aspring.step_02_hmm_maker.parse_args(args)

aspring.step_02_hmm_maker.run()

aspring.step_03_hmm_aligner module

aspring.step_03_hmm_aligner.get_arg_parser()

aspring.step_03_hmm_aligner.hmm_aligner(gene, msa_id_threshold, path_data, re_align, glo_loc, mact)

HMM-HMM profile alignment of all s-exons combinations for a chosen gene

aspring.step_03_hmm_aligner.parse_args(args)

aspring.step_03_hmm_aligner.run()

aspring.step_04_gettable module

aspring.step_04_gettable.dupraw2table(path_data, gene)

aspring.step_04_gettable.get_arg_parser()

aspring.step_04_gettable.hhr2df(path, gene)

aspring.step_04_gettable.parse_args(args)

aspring.step_04_gettable.read_fasta(fasta_file, keep_annotation=False)

Read sequences from fasta file.

Parameters:

• fasta_file (str) – Name of fasta file to read.

• keep_annotation (boolean) – Determine is sequence id should contain annotation.

Returns:

dict – Sequences indexed by sequence id.

Return type:

dict[seq_id] -> seq

aspring.step_04_gettable.run()

aspring.step_05_filter module

aspring.step_05_filter.filter(gene, path_data, id_pair, idCons_pair, pval, nbSpe, cov)

aspring.step_05_filter.get_arg_parser()

aspring.step_05_filter.parse_args(args)

aspring.step_05_filter.run()

aspring.step_06_stats module

This scripts runs the step_06_getStats.R script

aspring.step_06_stats.get_arg_parser()

aspring.step_06_stats.parse_args(args)

aspring.step_06_stats.run()

aspring.step_06_stats.run_r_script(gene, path_data)

aspring.step_06_stats.test_rscript_availability()

aspring.step_07_reformat module

aspring.step_07_reformat.get_arg_parser()

aspring.step_07_reformat.parse_args(args)

aspring.step_07_reformat.reformate(gene, path_data)

aspring.step_07_reformat.run()

aspring.step_08_ASRUs module

aspring.step_08_ASRUs.ases_df(path_data, gene)

aspring.step_08_ASRUs.codage(eve2pair, C, d_X)

aspring.step_08_ASRUs.event_to_pairs(path_data, G, gene)

aspring.step_08_ASRUs.eventsDup_df(path_data, gene)

aspring.step_08_ASRUs.extension_marge_pair(G, A, B, eveDups)

aspring.step_08_ASRUs.extensionbis(path_data, gene)

aspring.step_08_ASRUs.get_alnCols(G, A, B, eveDups)

aspring.step_08_ASRUs.get_arg_parser()

aspring.step_08_ASRUs.parse_args(args)

aspring.step_08_ASRUs.run()

aspring.step_08_ASRUs.sexSize(path_data, gene, sex)

aspring.step_08_ASRUs.sim_graph_initial(path_data, gene)

aspring.step_08_ASRUs.sim_graph_initial_bis(path_data, gene)

aspring.step_08_ASRUs.sim_graph_workframe(path_data, gene)

aspring.step_08_ASRUs.writecsv_ASRU(path_data, gene)

aspring.step_09_clean module

aspring.step_09_clean.get_arg_parser()

aspring.step_09_clean.parse_args(args)

aspring.step_09_clean.rm_tempfiles(gene, path_data)

aspring.step_09_clean.run()

aspring.step_10_struct module

aspring.step_10_struct.download_alphafold_structure(uniprot_id, output_path='.')

aspring.step_10_struct.download_pdb_structures(s_exon_table, output_path='.')

aspring.step_10_struct.get_arg_parser()

aspring.step_10_struct.get_asrus(asruFname)

aspring.step_10_struct.get_pdb_sequence_length(pdb)

aspring.step_10_struct.get_pdb_span(pdb)

aspring.step_10_struct.get_sexon_coord(gid, tid, seqFname)

aspring.step_10_struct.get_sexon_id(dictFname)

aspring.step_10_struct.get_transcript_sequence_length(gid, tid, seqFname)

aspring.step_10_struct.get_transcripts(s_exon_table)

aspring.step_10_struct.get_uniprot_id_from_filename(pdb_filename)

aspring.step_10_struct.get_uniprot_ids(species_gene_transcript_ids)

aspring.step_10_struct.parse_args(args)

aspring.step_10_struct.run()

aspring.step_10_struct.write_pml(coord, d, asrus, pdb, outname)

Module contents