├── CRISPRtracrRNA.py ├── LICENSE ├── README.md ├── environment.yml ├── modules ├── __init__.py ├── anti_repeat_search.py ├── argument_parser.py ├── candidate_ranking.py ├── candidates_based_on_anti_repeat.py ├── complete_terminator_search.py ├── consistency_score_maker.py ├── crispr_identify_summary_parser.py ├── folder_maker.py ├── general_helpers.py ├── hmm_model_run.py ├── intarna_run.py ├── model_run_only.py ├── pattern_search.py ├── pipelines.py └── run_identify_and_identifyer.py ├── test_input_complete ├── AAAIBU010000002.fasta └── AAAKQV010000004.fasta ├── test_input_model_only ├── AAAABK010000004.fasta ├── AAAABS010000003.fasta ├── AAAABU010000051.fasta ├── AAAABZ010000001.fasta ├── AAAACA010000003.fasta ├── AAAACD010000003.fasta ├── AAAACG010000004.fasta ├── AAAACI010000008.fasta ├── AAAACV010000002.fasta └── AAAAEB010000002.fasta ├── test_input_model_only_type_v ├── AAXW01000027.fasta ├── AP014815.fasta └── AP014821.fasta └── tools ├── CRISPRcasIdentifier └── description.txt ├── CRISPRidentify └── description.txt ├── cov_matrix ├── s2_b14 │ ├── cov_matrix.cm │ ├── cov_matrix.cm.i1f │ ├── cov_matrix.cm.i1i │ ├── cov_matrix.cm.i1m │ └── cov_matrix.cm.i1p └── type_5 │ ├── cluster1.top30.cm │ ├── cluster1.top30.cm.i1f │ ├── cluster1.top30.cm.i1i │ ├── cluster1.top30.cm.i1m │ ├── cluster1.top30.cm.i1p │ ├── cluster2.top30.cm │ ├── cluster2.top30.cm.i1f │ ├── cluster2.top30.cm.i1i │ ├── cluster2.top30.cm.i1m │ ├── cluster2.top30.cm.i1p │ ├── cluster3.top30.cm │ ├── cluster3.top30.cm.i1f │ ├── cluster3.top30.cm.i1i │ ├── cluster3.top30.cm.i1m │ ├── cluster3.top30.cm.i1p │ ├── cluster4.top30.cm │ ├── cluster4.top30.cm.i1f │ ├── cluster4.top30.cm.i1i │ ├── cluster4.top30.cm.i1m │ ├── cluster4.top30.cm.i1p │ ├── cov_matrix.cm │ ├── cov_matrix.cm.i1f │ ├── cov_matrix.cm.i1i │ ├── cov_matrix.cm.i1m │ └── cov_matrix.cm.i1p └── erpin ├── erpin └── rho-indep.epn /CRISPRtracrRNA.py: -------------------------------------------------------------------------------- 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