This module contains a class, Primer3InputTag, to standardize user input to Primer3. Settings that
are controlled here include general parameters that apply to a singular Primer3 session
as well as query-specific settings that can be changed in between primer queries.
Bases: UppercaseStrEnum
Enumeration of Primer3 input tags.
Please see the Primer3 manual for additional details
https://primer3.org/manual.html#commandLineTags
This class represents two categories of Primer3 input tags
SEQUENCE_ tags are those that control sequence-specific attributes of Primer3 jobs.
These can be modified after each query submitted to Primer3.PRIMER_ tags are those that describe more general parameters of Primer3 jobs.
These attributes persist across queries to Primer3 unless they are explicitly reset.
Errors in these "global" input tags are fatal.
Source code in prymer/primer3/primer3_input_tag.py
| @unique
class Primer3InputTag(UppercaseStrEnum):
"""
Enumeration of Primer3 input tags.
Please see the Primer3 manual for additional details:
https://primer3.org/manual.html#commandLineTags
This class represents two categories of Primer3 input tags:
* `SEQUENCE_` tags are those that control sequence-specific attributes of Primer3 jobs.
These can be modified after each query submitted to Primer3.
* `PRIMER_` tags are those that describe more general parameters of Primer3 jobs.
These attributes persist across queries to Primer3 unless they are explicitly reset.
Errors in these "global" input tags are fatal.
"""
# Sequence input tags; query-specific
SEQUENCE_EXCLUDED_REGION = auto()
SEQUENCE_INCLUDED_REGION = auto()
SEQUENCE_PRIMER_REVCOMP = auto()
SEQUENCE_FORCE_LEFT_END = auto()
SEQUENCE_INTERNAL_EXCLUDED_REGION = auto()
SEQUENCE_QUALITY = auto()
SEQUENCE_FORCE_LEFT_START = auto()
SEQUENCE_INTERNAL_OLIGO = auto()
SEQUENCE_START_CODON_POSITION = auto()
SEQUENCE_FORCE_RIGHT_END = auto()
SEQUENCE_OVERLAP_JUNCTION_LIST = auto()
SEQUENCE_TARGET = auto()
SEQUENCE_FORCE_RIGHT_START = auto()
SEQUENCE_PRIMER = auto()
SEQUENCE_TEMPLATE = auto()
SEQUENCE_ID = auto()
SEQUENCE_PRIMER_PAIR_OK_REGION_LIST = auto()
# Global input tags; will persist across primer3 queries
PRIMER_DNA_CONC = auto()
PRIMER_MAX_END_GC = auto()
PRIMER_PAIR_WT_PRODUCT_SIZE_LT = auto()
PRIMER_DNTP_CONC = auto()
PRIMER_MAX_END_STABILITY = auto()
PRIMER_PAIR_WT_PRODUCT_TM_GT = auto()
PRIMER_EXPLAIN_FLAG = auto()
PRIMER_MAX_GC = auto()
PRIMER_PAIR_WT_PRODUCT_TM_LT = auto()
PRIMER_FIRST_BASE_INDEX = auto()
PRIMER_MAX_HAIRPIN_TH = auto()
PRIMER_PAIR_WT_PR_PENALTY = auto()
PRIMER_GC_CLAMP = auto()
PRIMER_MAX_LIBRARY_MISPRIMING = auto()
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING = auto()
PRIMER_INSIDE_PENALTY = auto()
PRIMER_MAX_NS_ACCEPTED = auto()
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH = auto()
PRIMER_INTERNAL_DNA_CONC = auto()
PRIMER_MAX_POLY_X = auto()
PRIMER_PICK_ANYWAY = auto()
PRIMER_INTERNAL_DNTP_CONC = auto()
PRIMER_MAX_SELF_ANY = auto()
PRIMER_PICK_INTERNAL_OLIGO = auto()
PRIMER_INTERNAL_MAX_GC = auto()
PRIMER_MAX_SELF_ANY_TH = auto()
PRIMER_PICK_LEFT_PRIMER = auto()
PRIMER_INTERNAL_MAX_HAIRPIN_TH = auto()
PRIMER_MAX_SELF_END = auto()
PRIMER_PICK_RIGHT_PRIMER = auto()
PRIMER_INTERNAL_MAX_LIBRARY_MISHYB = auto()
PRIMER_MAX_SELF_END_TH = auto()
PRIMER_PRODUCT_MAX_TM = auto()
PRIMER_INTERNAL_MAX_NS_ACCEPTED = auto()
PRIMER_MAX_SIZE = auto()
PRIMER_PRODUCT_MIN_TM = auto()
PRIMER_INTERNAL_MAX_POLY_X = auto()
PRIMER_MAX_TEMPLATE_MISPRIMING = auto()
PRIMER_PRODUCT_OPT_SIZE = auto()
PRIMER_INTERNAL_MAX_SELF_ANY = auto()
PRIMER_MAX_TEMPLATE_MISPRIMING_TH = auto()
PRIMER_PRODUCT_OPT_TM = auto()
PRIMER_INTERNAL_MAX_SELF_ANY_TH = auto()
PRIMER_MAX_TM = auto()
PRIMER_PRODUCT_SIZE_RANGE = auto()
PRIMER_INTERNAL_MAX_SELF_END = auto()
PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION = auto()
PRIMER_QUALITY_RANGE_MAX = auto()
PRIMER_INTERNAL_MAX_SELF_END_TH = auto()
PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION = auto()
PRIMER_QUALITY_RANGE_MIN = auto()
PRIMER_INTERNAL_MAX_SIZE = auto()
PRIMER_MIN_END_QUALITY = auto()
PRIMER_SALT_CORRECTIONS = auto()
PRIMER_INTERNAL_MAX_TM = auto()
PRIMER_MIN_GC = auto()
PRIMER_SALT_DIVALENT = auto()
PRIMER_INTERNAL_MIN_GC = auto()
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE = auto()
PRIMER_SALT_MONOVALENT = auto()
PRIMER_INTERNAL_MIN_QUALITY = auto()
PRIMER_MIN_QUALITY = auto()
PRIMER_SEQUENCING_ACCURACY = auto()
PRIMER_INTERNAL_MIN_SIZE = auto()
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE = auto()
PRIMER_SEQUENCING_INTERVAL = auto()
PRIMER_INTERNAL_MIN_TM = auto()
PRIMER_MIN_SIZE = auto()
PRIMER_SEQUENCING_LEAD = auto()
PRIMER_INTERNAL_MISHYB_LIBRARY = auto()
PRIMER_MIN_THREE_PRIME_DISTANCE = auto()
PRIMER_SEQUENCING_SPACING = auto()
PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME = auto()
PRIMER_MIN_TM = auto()
PRIMER_TASK = auto()
PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME = auto()
PRIMER_MISPRIMING_LIBRARY = auto()
PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT = auto()
PRIMER_INTERNAL_OPT_GC_PERCENT = auto()
PRIMER_MUST_MATCH_FIVE_PRIME = auto()
PRIMER_THERMODYNAMIC_PARAMETERS_PATH = auto()
PRIMER_INTERNAL_OPT_SIZE = auto()
PRIMER_MUST_MATCH_THREE_PRIME = auto()
PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT = auto()
PRIMER_INTERNAL_OPT_TM = auto()
PRIMER_NUM_RETURN = auto()
PRIMER_TM_FORMULA = auto()
PRIMER_INTERNAL_SALT_DIVALENT = auto()
PRIMER_OPT_GC_PERCENT = auto()
PRIMER_WT_END_QUAL = auto()
PRIMER_INTERNAL_SALT_MONOVALENT = auto()
PRIMER_OPT_SIZE = auto()
PRIMER_WT_END_STABILITY = auto()
PRIMER_INTERNAL_WT_END_QUAL = auto()
PRIMER_OPT_TM = auto()
PRIMER_WT_GC_PERCENT_GT = auto()
PRIMER_INTERNAL_WT_GC_PERCENT_GT = auto()
PRIMER_OUTSIDE_PENALTY = auto()
PRIMER_WT_GC_PERCENT_LT = auto()
PRIMER_INTERNAL_WT_GC_PERCENT_LT = auto()
PRIMER_PAIR_MAX_COMPL_ANY = auto()
PRIMER_WT_HAIRPIN_TH = auto()
PRIMER_INTERNAL_WT_HAIRPIN_TH = auto()
PRIMER_PAIR_MAX_COMPL_ANY_TH = auto()
PRIMER_WT_LIBRARY_MISPRIMING = auto()
PRIMER_INTERNAL_WT_LIBRARY_MISHYB = auto()
PRIMER_PAIR_MAX_COMPL_END = auto()
PRIMER_WT_NUM_NS = auto()
PRIMER_INTERNAL_WT_NUM_NS = auto()
PRIMER_PAIR_MAX_COMPL_END_TH = auto()
PRIMER_WT_POS_PENALTY = auto()
PRIMER_INTERNAL_WT_SELF_ANY = auto()
PRIMER_PAIR_MAX_DIFF_TM = auto()
PRIMER_WT_SELF_ANY = auto()
PRIMER_INTERNAL_WT_SELF_ANY_TH = auto()
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING = auto()
PRIMER_WT_SELF_ANY_TH = auto()
PRIMER_INTERNAL_WT_SELF_END = auto()
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING = auto()
PRIMER_WT_SELF_END = auto()
PRIMER_INTERNAL_WT_SELF_END_TH = auto()
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH = auto()
PRIMER_WT_SELF_END_TH = auto()
PRIMER_INTERNAL_WT_SEQ_QUAL = auto()
PRIMER_PAIR_WT_COMPL_ANY = auto()
PRIMER_WT_SEQ_QUAL = auto()
PRIMER_INTERNAL_WT_SIZE_GT = auto()
PRIMER_PAIR_WT_COMPL_ANY_TH = auto()
PRIMER_WT_SIZE_GT = auto()
PRIMER_INTERNAL_WT_SIZE_LT = auto()
PRIMER_PAIR_WT_COMPL_END = auto()
PRIMER_WT_SIZE_LT = auto()
PRIMER_INTERNAL_WT_TM_GT = auto()
PRIMER_PAIR_WT_COMPL_END_TH = auto()
PRIMER_WT_TEMPLATE_MISPRIMING = auto()
PRIMER_INTERNAL_WT_TM_LT = auto()
PRIMER_PAIR_WT_DIFF_TM = auto()
PRIMER_WT_TEMPLATE_MISPRIMING_TH = auto()
PRIMER_LIBERAL_BASE = auto()
PRIMER_PAIR_WT_IO_PENALTY = auto()
PRIMER_WT_TM_GT = auto()
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS = auto()
PRIMER_PAIR_WT_LIBRARY_MISPRIMING = auto()
PRIMER_WT_TM_LT = auto()
PRIMER_LOWERCASE_MASKING = auto()
PRIMER_PAIR_WT_PRODUCT_SIZE_GT = auto()
|