pygor3.scripts package¶
Submodules¶
pygor3.scripts.all_gene_alignments_id module¶
- pygor3.scripts.all_gene_alignments_id.generate_str_fasta(indexed_sequence, list_vdj_alignments: dict)¶
Given an Sequence index and the corresponding alignments vj/ vdj return a string with considering only offset
- pygor3.scripts.all_gene_alignments_id.get_V_anchor_index_in_seq_from_gene(align: pygor3.IgorIO.IgorAlignment_data)¶
- pygor3.scripts.all_gene_alignments_id.main()¶
pygor3.scripts.bs_pairwise_prob module¶
- pygor3.scripts.bs_pairwise_prob.get_pairwise_prob(mdl, event_nickname1, event_nickname2)¶
- pygor3.scripts.bs_pairwise_prob.main()¶
pygor3.scripts.cli module¶
pygor3.scripts.download_imgt_gene_templates module¶
- pygor3.scripts.download_imgt_gene_templates.main()¶
pygor3.scripts.get_imgt_data module¶
Created on Mon Aug 12 18:58:54 2019
@author: alfaceor
- pygor3.scripts.get_imgt_data.main()¶
pygor3.scripts.model_export module¶
Export Igor Model to csv files.
- pygor3.scripts.model_export.main()¶
pygor3.scripts.naive_align module¶
- pygor3.scripts.naive_align.generate_csv_line(indexed_sequence: <module 'pygor3.IgorIndexedSequence' from '/home/docs/checkouts/readthedocs.org/user_builds/pygor3/checkouts/latest/pygor3/IgorIndexedSequence.py'>, indexed_cdr3_record: list, list_vdj_alignments: dict, sep=';', header_list=['sequence_id', 'sequence', 'v_call', 'd_call', 'j_call', 'v_score', 'd_score', 'j_score'])¶
- pygor3.scripts.naive_align.generate_str_fasta_simple(indexed_sequence, list_vdj_alignments: dict)¶
Given an Sequence index and the corresponding alignments vj/ vdj return a string with considering only offset
- pygor3.scripts.naive_align.main()¶
pygor3.scripts.naive_align_id module¶
- pygor3.scripts.naive_align_id.generate_csv_line(indexed_sequence: <module 'pygor3.IgorIndexedSequence' from '/home/docs/checkouts/readthedocs.org/user_builds/pygor3/checkouts/latest/pygor3/IgorIndexedSequence.py'>, list_vdj_alignments: dict, sep=';', header_list=['sequence_id', 'sequence', 'v_call', 'd_call', 'j_call', 'v_score', 'd_score', 'j_score', 'junction'])¶
- pygor3.scripts.naive_align_id.generate_str_fasta(indexed_sequence, list_vdj_alignments: dict)¶
Given an Sequence index and the corresponding alignments vj/ vdj return a string with considering only offset
- pygor3.scripts.naive_align_id.generate_str_fasta_simple(indexed_sequence, list_vdj_alignments: dict)¶
Given an Sequence index and the corresponding alignments vj/ vdj return a string with considering only offset
- pygor3.scripts.naive_align_id.main()¶
pygor3.scripts.observable module¶
- pygor3.scripts.observable.calc_average(db: pygor3.IgorSqliteDB.IgorSqliteDB, observable_function)¶
- pygor3.scripts.observable.generate_event_delta_Kronecker(event_nickname, event_id)¶
- pygor3.scripts.observable.main()¶
- pygor3.scripts.observable.main_old()¶
- pygor3.scripts.observable.observable()¶
Get a observable file or database, dataframe, etc … return the result of the observable defined
pygor3.scripts.plot_marginals module¶
Export Igor Model to csv files.
- pygor3.scripts.plot_marginals.main()¶
pygor3.scripts.scriptTest module¶
- pygor3.scripts.scriptTest.calc_average(db: pygor3.IgorSqliteDB.IgorSqliteDB, observable_function)¶
- pygor3.scripts.scriptTest.generate_event_delta_Kronecker(event_nickname, event_id)¶
- pygor3.scripts.scriptTest.get_pairwise_prob(mdl, event_nickname1, event_nickname2)¶
- pygor3.scripts.scriptTest.main()¶
pygor3.scripts.scriptTest02 module¶
- pygor3.scripts.scriptTest02.get_CDR3_data(mdl, scen)¶
- pygor3.scripts.scriptTest02.main()¶