Index

A

average_word_vectors() (phages2050.features.transformers.kmers.GenomeAvgTransformer method)

averaged_word_vectorizer() (phages2050.features.transformers.kmers.GenomeAvgTransformer method)

B

BacteriophageStructuralProteinClassifier (class in phages2050.classifiers.proteins.structural_protein) BacteriophageStructuralProteinManager (class in phages2050.classifiers.proteins.structural_protein)

BSP_LABELS_URL (phages2050.classifiers.proteins.structural_protein.BacteriophageStructuralProteinManager attribute) BSP_MODEL_URL (phages2050.classifiers.proteins.structural_protein.BacteriophageStructuralProteinManager attribute)

D

download_model() (phages2050.classifiers.proteins.structural_protein.BacteriophageStructuralProteinManager method) (phages2050.embeddings.nucleotides.word2vec.Word2VecModelManager method)

F

FastaReader (class in phages2050.features.io.fasta)

FEATURE_NAMES (phages2050.features.extractors.proteins.ProteinFeatureExtractor attribute) FEATURE_SPACE (phages2050.classifiers.proteins.structural_protein.BacteriophageStructuralProteinClassifier attribute)

G

GenomeAvgTransformer (class in phages2050.features.transformers.kmers) get_features() (phages2050.features.extractors.proteins.ProteinFeatureExtractor method)

get_sequence() (phages2050.features.io.fasta.FastaReader method) get_train_params() (phages2050.embeddings.nucleotides.word2vec.Word2VecEmbedding method)

K

KMersTransformer (class in phages2050.features.transformers.kmers)

M

MillardLabPhagesCrawler (class in phages2050.crawlers.millardlab.crawler)

MultifastaProteinFeatureExtractor (class in phages2050.features.extractors.proteins)

P

phages2050 (module) phages2050.classifiers (module) phages2050.classifiers.proteins (module) phages2050.classifiers.proteins.structural_protein (module) phages2050.crawlers (module) phages2050.crawlers.millardlab (module) phages2050.crawlers.millardlab.crawler (module) phages2050.crawlers.ncbi (module) phages2050.embeddings (module) phages2050.embeddings.nucleotides (module)

phages2050.embeddings.nucleotides.word2vec (module) phages2050.embeddings.proteins (module) phages2050.features (module) phages2050.features.extractors (module) phages2050.features.extractors.proteins (module) phages2050.features.io (module) phages2050.features.io.fasta (module) phages2050.features.transformers (module) phages2050.features.transformers.kmers (module) predict() (phages2050.classifiers.proteins.structural_protein.BacteriophageStructuralProteinClassifier method) ProteinFeatureExtractor (class in phages2050.features.extractors.proteins)

S

STATUS_CODE_200 (phages2050.classifiers.proteins.structural_protein.BacteriophageStructuralProteinManager attribute) (phages2050.embeddings.nucleotides.word2vec.Word2VecModelManager attribute)

SUPPORTED_COLUMNS (phages2050.classifiers.proteins.structural_protein.BacteriophageStructuralProteinClassifier attribute)

T

to_csv() (phages2050.crawlers.millardlab.crawler.MillardLabPhagesCrawler method) (phages2050.features.extractors.proteins.MultifastaProteinFeatureExtractor method) to_df() (phages2050.crawlers.millardlab.crawler.MillardLabPhagesCrawler method) (phages2050.features.extractors.proteins.MultifastaProteinFeatureExtractor method) (phages2050.features.io.fasta.FastaReader method)

transform() (phages2050.features.transformers.kmers.GenomeAvgTransformer method) (phages2050.features.transformers.kmers.KMersTransformer method)

W

WORD2VEC_URL (phages2050.embeddings.nucleotides.word2vec.Word2VecModelManager attribute)

Word2VecEmbedding (class in phages2050.embeddings.nucleotides.word2vec) Word2VecModelManager (class in phages2050.embeddings.nucleotides.word2vec)