bioforge 2.3.0__py3-none-win_amd64.whl
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- bioforge-2.3.0.data/purelib/bioforge/__init__.py +74 -0
- bioforge-2.3.0.data/purelib/bioforge/aligner.py +953 -0
- bioforge-2.3.0.data/purelib/bioforge/analyze.py +385 -0
- bioforge-2.3.0.data/purelib/bioforge/bgzf.py +119 -0
- bioforge-2.3.0.data/purelib/bioforge/biocore.py +2092 -0
- bioforge-2.3.0.data/purelib/bioforge/engine/__init__.py +1 -0
- bioforge-2.3.0.data/purelib/bioforge/engine/_loader.py +543 -0
- bioforge-2.3.0.data/purelib/bioforge/engine/build.py +231 -0
- bioforge-2.3.0.data/purelib/bioforge/engine/engine.c +1538 -0
- bioforge-2.3.0.data/purelib/bioforge/engine/engine.dll +0 -0
- bioforge-2.3.0.data/purelib/bioforge/qcreport.py +298 -0
- bioforge-2.3.0.data/purelib/bioforge/smart_translator.py +601 -0
- bioforge-2.3.0.dist-info/METADATA +736 -0
- bioforge-2.3.0.dist-info/RECORD +18 -0
- bioforge-2.3.0.dist-info/WHEEL +5 -0
- bioforge-2.3.0.dist-info/entry_points.txt +4 -0
- bioforge-2.3.0.dist-info/licenses/LICENSE +280 -0
- bioforge-2.3.0.dist-info/top_level.txt +1 -0
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"""
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BioForge — high-performance bioinformatics engine for Edge Computing.
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Quick start
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-----------
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>>> from bioforge import SmartImporter, SmartTranslator, SequenceAligner, SeqType
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>>> seqs = SmartImporter.from_string(">gene\\nATGAAAGGGTAA\\n")
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>>> prot = SmartTranslator.translate(seqs[0])
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>>> prot.to_string()
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'MKG'
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"""
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from .aligner import AlignmentResult, Mutation, SequenceAligner, format_alignment
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from .analyze import AnalysisResult, build_report, run
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from .biocore import (
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AA_LUT,
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NUC_LUT,
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AlignmentError,
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BioCode,
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BioForgeError,
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BioForgeIOError,
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BitPacker,
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EngineError,
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FastqRecord,
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PackedSequence,
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ReadBatch,
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SeqType,
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SequenceBatch,
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SequenceStats,
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SequenceTypeError,
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SequenceValueError,
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SmartImporter,
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TranslationError,
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compute_stats,
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)
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from .smart_translator import SmartTranslator
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__version__ = "2.3.0"
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__author__ = "Aarón Aranda Torrijos"
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__all__ = [
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# Exceptions
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"BioForgeError",
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"SequenceTypeError",
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"SequenceValueError",
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"TranslationError",
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"AlignmentError",
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"BioForgeIOError",
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"EngineError",
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# Core types
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"BioCode",
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"SeqType",
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"NUC_LUT",
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"AA_LUT",
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"BitPacker",
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"PackedSequence",
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"FastqRecord",
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"SequenceBatch",
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"ReadBatch",
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"SmartImporter",
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"SequenceStats",
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"compute_stats",
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# Translator
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"SmartTranslator",
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# Aligner
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"SequenceAligner",
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"format_alignment",
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"Mutation",
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"AlignmentResult",
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# Pipeline
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"run",
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"build_report",
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"AnalysisResult",
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]
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