+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ primerdriver.checks.PrimerChecks
+
+
+__init__(sequence, no_interaction=False)
+
+A set of validation checks to perform on the DNA/protein input before processing.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ sequence
+ |
+
+ str
+ |
+
+
+
+ The input DNA/protein sequence. + |
+ + required + | +
+ no_interaction
+ |
+ + | +
+
+
+ Suppress all prompts and use program defaults if not explicitly provided. + |
+
+ False
+ |
+
is_valid_dna()
+
+Check if the self.sequence contains valid bases [ATCG].
Raises:
+| Type | +Description | +
|---|---|
+ PrimerCheckError
+ |
+
+
+
+ DNA/protein sequence contains bases/amino acids. + |
+
Returns: + The input DNA sequence.
+ +is_valid_gc_content()
+
+Check if the self.sequence has valid %GC content (determined by settings.json).
Raises:
+| Type | +Description | +
|---|---|
+ PrimerCheckError
+ |
+
+
+
+ DNA/protein sequence has too little/too much GC content. + |
+
is_valid_protein()
+
+Check if the self.sequence contains valid amino acids.
Raises:
+| Type | +Description | +
|---|---|
+ PrimerCheckError
+ |
+
+
+
+ Protein sequence contains invalid amino acids. + |
+
Returns: + The input protein sequence.
+ +is_valid_sequence_length()
+
+Check if the self.sequence is within the allowed processing length (40 <= sequence <= 8000).
Raises:
+| Type | +Description | +
|---|---|
+ PrimerCheckError
+ |
+
+
+
+ DNA/protein sequence is too short/long. + |
+
primerdriver.checks.SequenceChecks
+
+
+__init__(sequence)
+
+Set of checks to perform on a generated primer.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ sequence
+ |
+
+ str | list[str]
+ |
+
+
+
+ The generated primer's DNA sequence. + |
+ + required + | +
primerdriver.exceptions.PrimerCheckError
+
+
+
+ Bases: ValueError
primerdriver.input_handler.interactive_handler()
+
+primerdriver.input_handler.single_command_handler(args)
+
+primerdriver.output_handler.interactive_saver(df)
+
+primerdriver.output_handler.single_command_saver(df, savename)
+
+primerdriver.primer_design.PrimerDesign
+
+
+calculate_gc_content(seq)
+
+
+ staticmethod
+
+
+Calculate the GC content of a sequence.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ seq
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to calculate the GC content of. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ float
+ |
+
+
+
+ The %GC content of the sequence. + |
+
calculate_melting_temperature(seq, mutation_type, replacement, gc_content, mismatch)
+
+
+ staticmethod
+
+
+Calculate the melting temperature of a sequence.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ seq
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to calculate the melting temperature of. + |
+ + required + | +
+ mutation_type
+ |
+
+ MutationType
+ |
+
+
+
+ The type of mutation (substitution, insertion, or deletion). + |
+ + required + | +
+ replacement
+ |
+
+ str | list[str]
+ |
+
+
+
+ The replacement sequence for the mutation. + |
+ + required + | +
+ gc_content
+ |
+
+ float
+ |
+
+
+
+ The %GC content of the sequence. + |
+ + required + | +
+ mismatch
+ |
+
+ float
+ |
+
+
+
+ The base mismatch percentage of the sequence. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ float
+ |
+
+
+
+ The melting temperature of the sequence in degrees Celsius. + |
+
calculate_mismatch(seq, mismatched_bases)
+
+
+ staticmethod
+
+
+Calculate the base mismatch percentage of a sequence.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ seq
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to calculate the mismatch percentage of. + |
+ + required + | +
+ mismatched_bases
+ |
+
+ int
+ |
+
+
+
+ The number of mismatched bases in the sequence. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ float
+ |
+
+
+
+ The base mismatch percentage of the sequence. + |
+
characterize_primer(sequence, mutation_type, replacement, mismatched_bases, index=None, reverse=None)
+
+Characterize a primer.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ sequence
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence of the primer. + |
+ + required + | +
+ mutation_type
+ |
+
+ MutationType
+ |
+
+
+
+ The type of mutation (substitution, insertion, or deletion). + |
+ + required + | +
+ replacement
+ |
+
+ str | list[str] | None
+ |
+
+
+
+ The replacement sequence for the mutation. + |
+ + required + | +
+ mismatched_bases
+ |
+
+ int
+ |
+
+
+
+ The number of mismatched bases in the sequence. + |
+ + required + | +
+ index
+ |
+
+ int | None
+ |
+
+
+
+ The index of the primer in the list of primers. + |
+
+ None
+ |
+
+ reverse
+ |
+
+ list[str] | None
+ |
+
+
+
+ The reverse complement of the sequence. + |
+
+ None
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ DataFrame
+ |
+
+
+
+ A DataFrame containing the characteristics of the primer. + |
+
deletion(sequence, mutation_type, target, replacement, start_position, mismatched_bases)
+
+Perform a deletion mutation.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ sequence
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence of the primer. + |
+ + required + | +
+ mutation_type
+ |
+
+ MutationType
+ |
+
+
+
+ The type of mutation. + |
+ + required + | +
+ target
+ |
+
+ str | list[str] | None
+ |
+
+
+
+ The target sequence. + |
+ + required + | +
+ replacement
+ |
+
+ str | list[str]
+ |
+
+
+
+ The replacement sequence. + |
+ + required + | +
+ start_position
+ |
+
+ int
+ |
+
+
+
+ The starting position of the mutation. + |
+ + required + | +
+ mismatched_bases
+ |
+
+ int
+ |
+
+
+
+ The number of mismatched bases. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ DataFrame | None
+ |
+
+
+
+ A DataFrame containing the characteristics of the generated primer(s). + |
+
dna_based()
+
+DNA based primer design.
+ +get_reverse_complement(seq)
+
+Get the reverse complement of a sequence.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ seq
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to get the reverse complement of. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ list[str]
+ |
+
+
+
+ The reverse complement of the sequence. + |
+
insertion(sequence, mutation_type, target, replacement, start_position, mismatched_bases)
+
+Perform an insertion mutation.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ sequence
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to mutate. + |
+ + required + | +
+ mutation_type
+ |
+
+ MutationType
+ |
+
+
+
+ The type of mutation to perform. + |
+ + required + | +
+ target
+ |
+
+ str | list[str] | None
+ |
+
+
+
+ The target sequence to insert into the sequence. + |
+ + required + | +
+ replacement
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to insert into the sequence. + |
+ + required + | +
+ start_position
+ |
+
+ int
+ |
+
+
+
+ The position to start the mutation. + |
+ + required + | +
+ mismatched_bases
+ |
+
+ int
+ |
+
+
+
+ The number of mismatched bases in the sequence. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ DataFrame | None
+ |
+
+
+
+ A DataFrame containing the characteristics of the generated primer(s). + |
+
is_gc_end(sequence)
+
+
+ staticmethod
+
+
+Check if a sequence starts/ends in G or C.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ sequence
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to check. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ bool
+ |
+
+
+
+ True if the sequence starts/ends in G or C, False otherwise. + |
+
protein_based()
+
+Protein based primer design.
+ +substitution(sequence, mutation_type, target, replacement, start_position, mismatched_bases)
+
+Performs a substitution mutation on a sequence.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ sequence
+ |
+
+ str | list[str]
+ |
+
+
+
+ The sequence to mutate. + |
+ + required + | +
+ mutation_type
+ |
+
+ MutationType
+ |
+
+
+
+ The type of mutation (substitution, insertion, or deletion). + |
+ + required + | +
+ target
+ |
+
+ str | list[str] | None
+ |
+
+
+
+ The target of the mutation. + |
+ + required + | +
+ replacement
+ |
+
+ str | list[str]
+ |
+
+
+
+ The replacement sequence for the mutation. + |
+ + required + | +
+ start_position
+ |
+
+ int
+ |
+
+
+
+ The starting position of the mutation. + |
+ + required + | +
+ mismatched_bases
+ |
+
+ int
+ |
+
+
+
+ The number of mismatched bases in the sequence. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ DataFrame | None
+ |
+
+
+
+ A DataFrame containing the characteristics of the generated primer(s). + |
+
primerdriver.primer_design.OperationMode
+
+
+
+ Bases: Enum
CHARACTERIZATION = 'CHAR'
+
+
+ class-attribute
+ instance-attribute
+
+
+DNA = 'DNA'
+
+
+ class-attribute
+ instance-attribute
+
+
+PROTEIN = 'PRO'
+
+
+ class-attribute
+ instance-attribute
+
+
+primerdriver.primer_design.MutationType
+
+
+
+ Bases: Enum
DELETION = 'D'
+
+
+ class-attribute
+ instance-attribute
+
+
+INSERTION = 'I'
+
+
+ class-attribute
+ instance-attribute
+
+
+SUBSTITUTION = 'S'
+
+
+ class-attribute
+ instance-attribute
+
+
+primerdriver.primer_design.PrimerMode
+
+
+
+ Bases: Enum
COMPLEMENTARY = 'complementary'
+
+
+ class-attribute
+ instance-attribute
+
+
+OVERLAPPING = 'overlapping'
+
+
+ class-attribute
+ instance-attribute
+
+
+