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pore_c.analyses.reference module

pore_c.analyses.reference.create_fragment_dataframe(seqid: str, seq: str, digest_type: str, digest_param: str) → pandas.core.frame.DataFrame

Iterate over the sequences in a fasta file and find the match positions for the restriction fragment

pore_c.analyses.reference.create_regex(pattern: str) → Pattern

Takes a raw restriction digest site in the form of a regular expression string and returns a regular expression object consisting of both forward and reverse complement versions of the pattern

pore_c.analyses.reference.create_virtual_digest(reference_fasta: pathlib.Path, digest_type: str, digest_param: str, fragments: Optional[pathlib.Path] = None, digest_stats: Optional[pathlib.Path] = None) → Tuple[FragmentRecordDf, pandas.core.frame.DataFrame]

Iterate over the sequences in a fasta file and find the match positions for the restriction fragment

pore_c.analyses.reference.find_fragment_intervals(digest_type: str, digest_param: str, seq: str) → List[int]

Finds the start positions of all matches of the regex in the sequence

pore_c.analyses.reference.find_site_positions_bins(bin_width, seq: str) → List[int]

Mimic a fixed-width sequence digest by returning the positions of fixed-width bin boundaries

pore_c.analyses.reference.find_site_positions_biopython(enzyme: str, seq: str) → List[int]

pore_c.analyses.reference.find_site_positions_regex(regex: Pattern, seq: str) → List[int]

Finds the start positions of all matches of the regex in the sequence

pore_c.analyses.reference.replace_degenerate(pattern: str) → str

Replace degenerate bases with regex set

pore_c.analyses.reference.revcomp(seq: str) → str

Return the reverse complement of a string:

pore_c.analyses.reference.to_intervals(positions: List[int], chrom_length: int)

pore_c.analyses.reads module pore_c.catalogs module