Module: Qu::Pcr
- Defined in:
- lib/qu/pcr.rb,
lib/qu/pcr/primer3.rb,
lib/qu/pcr/version.rb,
lib/qu/pcr/primer3_parameters.rb
Defined Under Namespace
Classes: Amplicon, Primer, Primer3, Primer3Parser, Product, VirtualGel
Constant Summary collapse
- VERSION =
"1.0.12"- PRIMER3_OPTIONS =
{ SEQUENCE_ID: "", SEQUENCE_TEMPLATE: "", SEQUENCE_INCLUDED_REGION: "", SEQUENCE_TARGET: "", SEQUENCE_EXCLUDED_REGION: "", SEQUENCE_PRIMER_PAIR_OK_REGION_LIST: "", SEQUENCE_OVERLAP_JUNCTION_LIST: "", SEQUENCE_INTERNAL_EXCLUDED_REGION: "", SEQUENCE_PRIMER: "", SEQUENCE_INTERNAL_OLIGO: "", SEQUENCE_PRIMER_REVCOMP: "", SEQUENCE_FORCE_LEFT_START: -1000000, SEQUENCE_FORCE_LEFT_END: -1000000, SEQUENCE_FORCE_RIGHT_START: -1000000, SEQUENCE_FORCE_RIGHT_END: -1000000, PRIMER_TASK: "generic", PRIMER_PICK_LEFT_PRIMER: 1, PRIMER_PICK_INTERNAL_OLIGO: 0, PRIMER_PICK_RIGHT_PRIMER: 1, PRIMER_NUM_RETURN: 10, PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION: 4, PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION: 7, PRIMER_MUST_MATCH_FIVE_PRIME: "", PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME: "", PRIMER_MUST_MATCH_THREE_PRIME: "", PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME: "", PRIMER_PRODUCT_SIZE_RANGE: "100-150 151-250 100-300 301-400 401-500 501-600 601-700 701-850 851-1000", PRIMER_PRODUCT_OPT_SIZE: 0, PRIMER_PAIR_WT_PRODUCT_SIZE_LT: 0.0, PRIMER_PAIR_WT_PRODUCT_SIZE_GT: 0.0, PRIMER_MIN_SIZE: 15, PRIMER_INTERNAL_MIN_SIZE: 18, PRIMER_OPT_SIZE: 22, PRIMER_INTERNAL_OPT_SIZE: 20, PRIMER_MAX_SIZE: 35, PRIMER_INTERNAL_MAX_SIZE: 35, # Customed by Wubin Qu PRIMER_WT_SIZE_LT: 0.0, PRIMER_INTERNAL_WT_SIZE_LT: 0.0, # Customed by Wubin Qu PRIMER_WT_SIZE_GT: 0.0, PRIMER_INTERNAL_WT_SIZE_GT: 0.0, PRIMER_MIN_GC: 20.0, PRIMER_INTERNAL_MIN_GC: 20.0, PRIMER_OPT_GC_PERCENT: 50.0, PRIMER_INTERNAL_OPT_GC_PERCENT: 50.0, PRIMER_MAX_GC: 80.0, PRIMER_INTERNAL_MAX_GC: 80.0, PRIMER_WT_GC_PERCENT_LT: 0.0, PRIMER_INTERNAL_WT_GC_PERCENT_LT: 0.0, PRIMER_WT_GC_PERCENT_GT: 0.0, PRIMER_INTERNAL_WT_GC_PERCENT_GT: 0.0, PRIMER_GC_CLAMP: 0, PRIMER_MAX_END_GC: 5, PRIMER_MIN_TM: 55.0, PRIMER_INTERNAL_MIN_TM: 55.0, PRIMER_OPT_TM: 62.0, PRIMER_INTERNAL_OPT_TM: 62.0, PRIMER_MAX_TM: 65.0, PRIMER_INTERNAL_MAX_TM: 65.0, PRIMER_PAIR_MAX_DIFF_TM: 10.0, PRIMER_WT_TM_LT: 1.0, PRIMER_INTERNAL_WT_TM_LT: 1.0, PRIMER_WT_TM_GT: 1.0, PRIMER_INTERNAL_WT_TM_GT: 1.0, PRIMER_PAIR_WT_DIFF_TM: 1.0, PRIMER_PRODUCT_MIN_TM: -1000000.0, PRIMER_PRODUCT_OPT_TM: 0.0, PRIMER_PRODUCT_MAX_TM: 1000000.0, PRIMER_PAIR_WT_PRODUCT_TM_LT: 0.0, PRIMER_PAIR_WT_PRODUCT_TM_GT: 0.0, PRIMER_TM_FORMULA: 1, PRIMER_SALT_MONOVALENT: 50.0, PRIMER_INTERNAL_SALT_MONOVALENT: 50.0, PRIMER_SALT_DIVALENT: 1.5, PRIMER_INTERNAL_SALT_DIVALENT: 0.0, # Customed by Wubin Qu PRIMER_DNTP_CONC: 0.25, PRIMER_INTERNAL_DNTP_CONC: 0.0, PRIMER_SALT_CORRECTIONS: 1, PRIMER_DNA_CONC: 50.0, PRIMER_INTERNAL_DNA_CONC: 50.0, PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT: 1, PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT: 1, PRIMER_THERMODYNAMIC_PARAMETERS_PATH: Cmdwrapper::THERMO_PATH, PRIMER_MAX_SELF_ANY: 8.00, PRIMER_MAX_SELF_ANY_TH: 47.00, PRIMER_INTERNAL_MAX_SELF_ANY: 12.00, PRIMER_INTERNAL_MAX_SELF_ANY_TH: 47.00, PRIMER_PAIR_MAX_COMPL_ANY: 8.00, PRIMER_PAIR_MAX_COMPL_ANY_TH: 47.00, PRIMER_WT_SELF_ANY: 0.0, PRIMER_WT_SELF_ANY_TH: 0.0, PRIMER_INTERNAL_WT_SELF_ANY: 0.0, PRIMER_INTERNAL_WT_SELF_ANY_TH: 0.0, PRIMER_PAIR_WT_COMPL_ANY: 0.0, PRIMER_PAIR_WT_COMPL_ANY_TH: 0.0, PRIMER_MAX_SELF_END: 3.0, PRIMER_MAX_SELF_END_TH: 47.00, PRIMER_INTERNAL_MAX_SELF_END: 12.00, PRIMER_INTERNAL_MAX_SELF_END_TH: 47.00, PRIMER_PAIR_MAX_COMPL_END: 3.00, PRIMER_PAIR_MAX_COMPL_END_TH: 47.00, PRIMER_WT_SELF_END: 0.0, PRIMER_WT_SELF_END_TH: 0.0, PRIMER_INTERNAL_WT_SELF_END: 0.0, PRIMER_INTERNAL_WT_SELF_END_TH: 0.0, PRIMER_PAIR_WT_COMPL_END: 0.0, PRIMER_PAIR_WT_COMPL_END_TH: 0.0, PRIMER_MAX_HAIRPIN_TH: 47.0, PRIMER_INTERNAL_MAX_HAIRPIN_TH: 47.0, PRIMER_WT_HAIRPIN_TH: 0.0, PRIMER_INTERNAL_WT_HAIRPIN_TH: 0.0, PRIMER_MAX_END_STABILITY: 100.0, PRIMER_WT_END_STABILITY: 0.0, PRIMER_MAX_NS_ACCEPTED: 0, PRIMER_INTERNAL_MAX_NS_ACCEPTED: 0, PRIMER_WT_NUM_NS: 0.0, PRIMER_INTERNAL_WT_NUM_NS: 0.0, PRIMER_MAX_POLY_X: 5, PRIMER_INTERNAL_MAX_POLY_X: 5, PRIMER_MIN_THREE_PRIME_DISTANCE: 1, PRIMER_PICK_ANYWAY: 0, PRIMER_LOWERCASE_MASKING: 1, PRIMER_EXPLAIN_FLAG: 1, PRIMER_LIBERAL_BASE: 0, PRIMER_FIRST_BASE_INDEX: 0, PRIMER_MAX_TEMPLATE_MISPRIMING: -1.00, PRIMER_MAX_TEMPLATE_MISPRIMING_TH: -1.00, PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING: -1.00, PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH: -1.00, PRIMER_WT_TEMPLATE_MISPRIMING: 0.0, PRIMER_WT_TEMPLATE_MISPRIMING_TH: 0.0, PRIMER_PAIR_WT_TEMPLATE_MISPRIMING: 0.0, PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH: 0.0, PRIMER_MISPRIMING_LIBRARY: "", PRIMER_INTERNAL_MISHYB_LIBRARY: "", PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS: 0, PRIMER_MAX_LIBRARY_MISPRIMING: 12.00, PRIMER_INTERNAL_MAX_LIBRARY_MISHYB: 12.00, PRIMER_PAIR_MAX_LIBRARY_MISPRIMING: 24.00, PRIMER_WT_LIBRARY_MISPRIMING: 0.0, PRIMER_INTERNAL_WT_LIBRARY_MISHYB: 0.0, PRIMER_PAIR_WT_LIBRARY_MISPRIMING: 0.0, PRIMER_MIN_QUALITY: 0, PRIMER_INTERNAL_MIN_QUALITY: 0, PRIMER_MIN_END_QUALITY: 0, PRIMER_QUALITY_RANGE_MIN: 0, PRIMER_QUALITY_RANGE_MAX: 100, PRIMER_WT_SEQ_QUAL: 0.0, PRIMER_INTERNAL_WT_SEQ_QUAL: 0.0, PRIMER_PAIR_WT_PR_PENALTY: 1.0, PRIMER_PAIR_WT_IO_PENALTY: 0.0, PRIMER_INSIDE_PENALTY: -1.0, PRIMER_OUTSIDE_PENALTY: 0.0, PRIMER_WT_POS_PENALTY: 1.0, PRIMER_SEQUENCING_LEAD: 50, PRIMER_SEQUENCING_SPACING: 500, PRIMER_SEQUENCING_INTERVAL: 250, PRIMER_SEQUENCING_ACCURACY: 20, PRIMER_WT_END_QUAL: 0.0, PRIMER_INTERNAL_WT_END_QUAL: 0.0, P3_FILE_FLAG: 0, }
- USER_SPECIFIC_OPTIONS =
Parameters not shown to users for editing
[ :SEQUENCE_ID, :SEQUENCE_TARGET, :SEQUENCE_EXCLUDED_REGION, :SEQUENCE_FORCE_LEFT_START, :SEQUENCE_FORCE_LEFT_END, :SEQUENCE_FORCE_RIGHT_START, :SEQUENCE_FORCE_RIGHT_END, :SEQUENCE_PRIMER, :SEQUENCE_PRIMER_REVCOMP, :PRIMER_PRODUCT_SIZE_RANGE, :PRIMER_MIN_SIZE, :PRIMER_OPT_SIZE, :PRIMER_MAX_SIZE, :PRIMER_MIN_TM, :PRIMER_OPT_TM, :PRIMER_MAX_TM, :PRIMER_MIN_GC, :PRIMER_OPT_GC, :PRIMER_MAX_GC, :PRIMER_MAX_POLY_X, :PRIMER_MAX_HAIRPIN_TH, # I think it's no needed here, becuse they should be checked in MFEprimer (>v3.0), Wubin Qu [2014-5-8] :PRIMER_MAX_SELF_ANY_TH, :PRIMER_MAX_SELF_END_TH, :PRIMER_PAIR_MAX_COMPL_ANY_TH, :PRIMER_PAIR_MAX_COMPL_END_TH, :PRIMER_PRODUCT_OPT_TM, :PRIMER_MAX_NS_ACCEPTED, ]