Problems¶
BAliBASE¶
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class
pym2sa.problem.BAliBASE.BAliBASE(balibase_instance: str, balibase_path: str, score_list: typing.List[pymsa.core.score.Score]) → None¶ Bases:
pym2sa.problem.MSA.MSACreates a new problem based on an instance of BAliBASE.
Parameters: - balibase_instance – Instance name (e.g., BB12010).
- balibase_path – Path containing two directories: bb_aligned, with the pre-computed alignments and bb_release, with the original sequences.
- score_list – List of scores.
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DATA_FILES= ['tfa_clu', 'tfa_muscle', 'tfa_kalign', 'tfa_retalign', 'fasta_aln', 'tfa_probcons', 'tfa_mafft', 'tfa_fsa']¶
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create_solution() → pym2sa.core.solution.MSASolution¶ Read and import an instance of BAliBASE.
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get_name() → str¶
Generic MSA¶
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class
pym2sa.problem.MSA.MSA(score_list: typing.List[pymsa.core.score.Score], sequences_without_gaps: typing.List[str], sequences_names: typing.List[str])¶ Bases:
pym2sa.core.problem.MSAProblemCreates a new generic MSA problem.
Parameters: - score_list – List of scores to evaluate MSAs.
- sequences_without_gaps – List of original sequences (without gaps).
- sequences_names – List of sequences names.
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create_solution() → pym2sa.core.solution.MSASolution¶
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evaluate(solution: pym2sa.core.solution.MSASolution) → pym2sa.core.solution.MSASolution¶ Evaluate a multiple sequence alignment solution.
Parameters: solution – MSA to evaluate.
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get_name() → str¶