mavevdf

mavedf features a MaveDf object and functions that can be performed on that object. It also features helper functions that may be useful to the user.

mavetools.mavedf.mutation_type.is_deletion(hgvs)

This function takes an hgvs formatted string and returns True if the hgvs string indicates there was a deletion.

Parameters:

hgvs (string) – hgvs formatted string

Returns:

deletion – True if hgvs string is indicates a deletion

Return type:

bool

mavetools.mavedf.mutation_type.is_substitution_one_base(hgvs)

This function takes an hgvs formatted string and returns True if the hgvs string indicates there was a substitution at one base of the codon.

Parameters:

hgvs (string) – hgvs formatted string

Returns:

sub_one – True if hgvs string is indicates a substitution at one base of codon

Return type:

bool

mavetools.mavedf.mutation_type.is_substitution_two_bases_nonadjacent(hgvs)

This function takes an hgvs formatted string and returns True if the hgvs string indicates there were substitutions (non-adjacent) in the codon.

Parameters:

hgvs (string) – hgvs formatted string

Returns:

sub_two – True if hgvs string is indicates a substitution at one base of codon

Return type:

bool

mavetools.mavedf.mutation_type.is_wild_type(hgvs)

This function takes an hgvs formatted string and returns True if the hgvs string indicates there was no change from the target sequence.

Parameters:

hgvs (string) – hgvs formatted string

Returns:

wt – True if hgvs string indicates wild type

Return type:

bool

mavetools.mavedf.legacy_to_mave_new.legacy_to_mave_hgvs_nt(legacy_hgvs)

This function converts a legacy hgvs_nt formatted string (i.e., c.[1C>A;2=;3=]) and converts it to the standard format (i.e., c.1delinsA). If string is already in standard format, the input string is returned as-is.

Parameters:

hgvs_legacy (string) – legacy format hgvs string

Returns:

mave_hgvs – standard format hgvs string or empty string if input string is in invalid format

Return type:

string