phages2050.features.io package

Submodules

phages2050.features.io.fasta module

class phages2050.features.io.fasta.FastaReader(fasta_file_path: str)

Bases: object

Universal class for reading FASTA files with genome or protein sequence or multi-FASTA with chunks of sequences

Example:

fname = ‘NC_001604.fasta’ fr = FastaReader(fname)

kmers_sequence = fr.get_sequence()

ks_df = fr.to_df()

get_sequence() → str

Final genome or protein sequence string after normalization

to_df() → pandas.core.frame.DataFrame

Return pandas DataFrame with k-mers sequence format what is expected by KMersTransformer

Module contents