pyprot.base package

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pyprot.base.aminoacid module

class AminoAcid(aminoAcid)

Bases: builtins.object

Represents one of the amino acids that can be found in genetic sequences. Can be one of the following : - any of the twenty amino acids - any of four combinations of possible amino acids - selenocysteine, pyrrolysine, a gap or termination codon The full list of possible amino acids is defined by AA_NAMES.

__init__(aminoAcid)

Creates an AminoAcid object representing one of the possible amino acids. @param aminoAcid can be the name of an amino acid, or an AminoAcid object (in which case a copy is created).

static getAllNames(nameMode='short')

Yields the names of all represented amino acids, excepting gaps and termination codons.

getName(nameMode='short')

static getNames(nameMode='short')

Yields the names of the 20 basic amino acids.

static getNamesInRange(startIndex, stopIndex, nameMode='short')

Yields the names of amino acids in AA_NAMES, from startIndex to stopIndex (excluded).

isGap()

True if this amino acid is a gap, false otherwise.

isTermination()

True if this amino acid is a termination codon, false otherwise.

pyprot.base.sequence module

class Sequence(aminoAcids=None, description='')

Bases: builtins.list

Represents a sequence of amino acids. Inherits from list, and ensures all items are of type AminoAcid.

__init__(aminoAcids=None, description='')

Creates a Sequence object that represents the amino acid sequence contained in aminoAcids. aminoAcids can be one of the following : - None, meaning the Sequence is empty (default) - an AminoAcid object - a string of X AminoAcid short (uppercase) names or 1 AminoAcid name - a list containing AminoAcid objects and/or strings of individual AminoAcid names

extend(aminoAcids)

Extends the base by adding ‘aminoAcids’ at its end. @param aminoAcids must be compatible with the Sequence constructor

getDescription()

Returns the base’s description.

insert(index, aminoAcids)

Inserts aminoAcids into the base at index ‘index’. List objects will not be embedded as is, instead their items will be inserted in the same order, individually. @param aminoAcids must be compatible with the Sequence constructor @param index is the index at which aminoAcids is inserted

setDescription(description)

Sets the base’s description

setNameMode(newMode)

Changes the name display mode to ‘newMode’.

setSeparator(newSep)

Changes the string that separates each displayed AminoAcid.

Module contents