pypath.utils.seq.Seq

class pypath.utils.seq.Seq(protein, sequence, isoform=1)

Bases: object

__init__(protein, sequence, isoform=1)

This class is to look up or match residues and regions in sequences of proteins, by default in the canonical sequence, and optionally in other isoforms.

Methods

__init__(protein, sequence[, isoform])	This class is to look up or match residues and regions in sequences of proteins, by default in the canonical sequence, and optionally in other isoforms.
add_seq(sequence, isoform)
export_fasta([fname, sequences])
findall(fragment)	Looks up a sequence fragment in the sequences.
get(start[, end, isoform])
get_biopython([isoform])
get_region([residue, start, end, flanking, ...])
has_isoform(isoform)
isoforms()
match(pattern, start[, end, isoform])
multiple_alignment(sequences[, outfile, ...])

findall(fragment)

Looks up a sequence fragment in the sequences. Yields tuples of isoform and offset.