Module dentist.util.fasta

Some functions to work with FASTA data.

Functions

NameDescription
complement(base) Get the complement of a DNA base. Only bases A, T, C, G (case-insensitive) will be translated; all other characters are left as is. Replacement preserves casing of the characters.
getFastaLength(fastaFile) Calculate the sequence length of the first record in fastaFile. Returns the length of the next record in fastaFile if it is a File object.
parseFasta(data) Convenience wrapper around Fasta!T(T data).
parseFastaRecord(data) Convenience wrapper around FastaRecord!T(T data).
parsePacBioHeader(header) Convenience wrapper around PacBioHeader!T(T header).
reverseComplement(sequence) Compute the reverse complement of a DNA sequence. Only bases A, T, C, G (case-insensitive) will be translated; all other characters are left as is. Replacement preserves casing of the characters.
reverseComplement(fastaRecord) Return a copy of fastaRecord with reverse-complemented sequence.
reverseComplementer(sequence) Compute the reverse complement of a DNA sequence. Only bases A, T, C, G (case-insensitive) will be translated; all other characters are left as is. Replacement preserves casing of the characters.

Structs

NameDescription
Fasta Gives access to FASTA data. Does not copy the input sequence.
FastaRecord Gives access to a single FASTA record. Does not copy the input sequence.
PacBioHeader Represents standard PacBio header format: >{smrtId}/{well}/{hqBegin}_{hqEnd} {readQuality}