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lib/Bio/Tools/Run/Primer3.pm  view on Meta::CPAN

sub _input_args {
	my($self) = shift;
	# just return functions that we can set and what they are 
	my %hash=(
	'PRIMER_SEQUENCE_ID'=>'(string, optional) an id. Optional. Note must be present if PRIMER_FILE_FLAG is set',
  'SEQUENCE'=>'(nucleotide sequence, REQUIRED) The sequence itself. Cannot contain newlines',
  'INCLUDED_REGION'=>'(interval, optional) Where to pick primers from. In form <start>,<length>. Based on zero indexing!',
  'TARGET'=>'(interval list, default empty) Regions that must be included in the product. The value should be a space-separated list of <start>,<length>',
  'EXCLUDED_REGION'=>'(interval list, default empty) Regions that must NOT be included in the product. The value should be a space-separated list of <start>,<length>',
  'PRIMER_COMMENT'=>'(string) This is ignored, so we will just save, and return it',
  'PRIMER_SEQUENCE_QUALITY'=>'(quality list, default empty) A list of space separated integers with one per base. Could adapt a Phred object to this.',
  'PRIMER_LEFT_INPUT'=>'(nucleotide sequence, default empty) If you know the left primer sequence, put it here',
  'PRIMER_RIGHT_INPUT'=>'(nucleotide sequence, default empty) If you know the right primer sequence, put it here',
  'PRIMER_START_CODON_POSITION'=>'(int, default -1000000) Location of known start codons for designing in frame primers.',
  'PRIMER_PICK_ANYWAY'=>'boolean, default 0) Pick a primer, even if we have violated some constraints.',
  'PRIMER_MISPRIMING_LIBRARY'=>'(string, optional) A file containing sequences to avoid amplifying. Should be fasta format, but see primer3 docs for constraints.',
  'PRIMER_MAX_MISPRIMING'=>'(decimal,9999.99, default 12.00) Weighting for PRIMER_MISPRIMING_LIBRARY',
  'PRIMER_PAIR_MAX_MISPRIMING'=>'(decimal,9999.99, default 24.00 Weighting for PRIMER_MISPRIMING_LIBRARY',
  'PRIMER_PRODUCT_MAX_TM'=>'(float, default 1000000.0) The maximum allowed Tm of the product.',
  'PRIMER_PRODUCT_MIN_TM'=>'(float, default -1000000.0) The minimum allowed Tm of the product',
  'PRIMER_EXPLAIN_FLAG'=>'(boolean, default 0) If set it will print a bunch of information out.',
  'PRIMER_PRODUCT_SIZE_RANGE'=>'(size range list, default 100-300) space separated list of product sizes eg <a>-<b> <x>-<y>',
  
  'PRIMER_DEFAULT_PRODUCT' => '(size range list, default 100-300)',
  'PRIMER_PICK_INTERNAL_OLIGO'=>'(boolean, default 0) if set, a hybridization probe will be selected',
  'PRIMER_GC_CLAMP'=>'(int, default 0) Number of Gs and Cs at the 3 prime end.',
  'PRIMER_OPT_SIZE'=>'(int, default 20) Optimal primer size. Primers will be close to this value in length',
  'PRIMER_DEFAULT_SIZE' => '(int, default 20)',
  'PRIMER_MIN_SIZE'=>'(int, default 18) Minimum size. Must be 0 < PRIMER_MIN_SIZE < PRIMER_MAX_SIZE ',
  'PRIMER_MAX_SIZE'=>'(int, default 27) Maximum size. Must be < 35.',
  'PRIMER_OPT_TM'=>'(float, default 60.0C) Optimum Tm of a primer.',
  'PRIMER_MIN_TM'=>'(float, default 57.0C) Minimum Tm of a primer',
  'PRIMER_MAX_TM'=>'(float, default 63.0C) Maximum Tm of a primer',
  'PRIMER_MAX_DIFF_TM'=>'(float, default 100.0C) acceptable difference in Tms',
  'PRIMER_MIN_GC'=>'(float, default 20.0%) Minimum allowable GCs',
  'PRIMER_OPT_GC_PERCENT'=>'(float, default 50.0%) Optimal GCs',
  'PRIMER_MAX_GC'=>'(float, default 80.0%) Maximum allowable GCs',
  'PRIMER_SALT_CONC'=>'(float, default 50.0 mM) Salt concentration required for Tm calcs.',
  'PRIMER_DNA_CONC'=>'(float, default 50.0 nM) DNA concentration required for Tm calcs. ',
  'PRIMER_NUM_NS_ACCEPTED'=>'(int, default 0) Maximum number of unknown bases (N) allowable in any primer.',
  'PRIMER_SELF_ANY'=>'(decimal,9999.99, default 8.00) Maximum aligment score for within and between primers when checking for hairpin loops',
  'PRIMER_SELF_END'=>'(decimal 9999.99, default 3.00) Maximum aligment score for within and between primers when checking for primer dimers',
  'PRIMER_FILE_FLAG'=>'(boolean, default 0) Output <sequence_id>.for and <sequence_id>.rev with all acceptable forward and reverse primers',
  'PRIMER_MAX_POLY_X'=>'(int, default 5) The maximum allowable length of a mononucleotide repeat.',
  'PRIMER_LIBERAL_BASE'=>'(boolean, default 0) Use IUPAC codes (well, just change them to N). Note must also set PRIMER_NUM_NS_ACCEPTED',
  'PRIMER_NUM_RETURN'=>'(int, default 5) Number of primers to return',
  'PRIMER_FIRST_BASE_INDEX'=>'(int, default 0) Index of the first base. Do not change this or allow it to be changed, as we will have to mess with subseqs and whatnot.',
  'PRIMER_MIN_QUALITY'=>'(int, default 0) Minimum sequence quality calculated from PRIMER_SEQUENCE_QUALITY',
  'PRIMER_MIN_END_QUALITY'=>'(int, default 0) Minimum sequence quality calculated from PRIMER_SEQUENCE_QUALITY at 5 prime 5 bases',
  'PRIMER_QUALITY_RANGE_MIN'=>'(int, default 0) Minimum sequence quality calculated from PRIMER_SEQUENCE_QUALITY',
  'PRIMER_QUALITY_RANGE_MAX'=>'(int, default 100) Maximum sequence quality calculated from PRIMER_SEQUENCE_QUALITY',
  'PRIMER_MAX_END_STABILITY'=>'(float 999.9999, default 100.0) Maximum stability for the five 3 prime bases of a primer. Bigger numbers mean more stable 3 prime ends.',
  'PRIMER_PRODUCT_OPT_TM'=>'(float, default 0.0) Optimum melting temperature for the PCR product. 0 means no optimum.',
  'PRIMER_PRODUCT_OPT_SIZE'=>'(int, default 0) Optimum size for the PCR product. 0 means no optimum.',
  'PRIMER_TASK'=>'(string, default pick_pcr_primers) Choose from pick_pcr_primers, pick_pcr_primers_and_hyb_probe, pick_left_only, pick_right_only, pick_hyb_probe_only',
  'PRIMER_WT_TM_GT'=>'(float, default 1.0) Penalty weight for primers with Tm over PRIMER_OPT_TM.',
  'PRIMER_WT_TM_LT'=>'(float, default 1.0) Penalty weight for primers with Tm under PRIMER_OPT_TM.',
  'PRIMER_WT_SIZE_LT'=>'(float, default 1.0) Penalty weight for primers shorter than PRIMER_OPT_SIZE.',
  'PRIMER_WT_SIZE_GT'=>'(float, default 1.0) Penalty weight for primers longer than PRIMER_OPT_SIZE.',
  'PRIMER_WT_GC_PERCENT_LT'=>'(float, default 1.0) Penalty weight for primers with GC percent greater than PRIMER_OPT_GC_PERCENT.',
  'PRIMER_WT_GC_PERCENT_GT'=>'(float, default 1.0) Penalty weight for primers with GC percent greater than PRIMER_OPT_GC_PERCENT.',
  'PRIMER_WT_COMPL_ANY'=>'(float, default 0.0)',
  'PRIMER_WT_COMPL_END'=>'(float, default 0.0)',
  'PRIMER_WT_NUM_NS'=>'(float, default 0.0)',
  'PRIMER_WT_REP_SIM'=>'(float, default 0.0)',
  'PRIMER_WT_SEQ_QUAL'=>'(float, default 0.0)',
  'PRIMER_WT_END_QUAL'=>'(float, default 0.0)',
  'PRIMER_WT_POS_PENALTY'=>'(float, default 0.0)',
  'PRIMER_WT_END_STABILITY'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_PR_PENALTY'=>'(float, default 1.0)',
  'PRIMER_PAIR_WT_IO_PENALTY'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_DIFF_TM'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_COMPL_ANY'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_COMPL_END'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_PRODUCT_TM_LT'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_PRODUCT_TM_GT'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_PRODUCT_SIZE_GT'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_PRODUCT_SIZE_LT'=>'(float, default 0.0)',
  'PRIMER_PAIR_WT_REP_SIM'=>'(float, default 0.0)',
  'PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION'=>'(interval list, default empty) Internal oligos must ignore these regions',
  'PRIMER_INTERNAL_OLIGO_INPUT'=>'(nucleotide sequence, default empty) Known sequence of an internal oligo',
  'PRIMER_INTERNAL_OLIGO_OPT_SIZE'=>'(int, default 20)',
  'PRIMER_INTERNAL_OLIGO_MIN_SIZE'=>'(int, default 18)',
  'PRIMER_INTERNAL_OLIGO_MAX_SIZE'=>'(int, default 27)',
  'PRIMER_INTERNAL_OLIGO_OPT_TM'=>'(float, default 60.0 degrees C)',
  'PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT'=>'(float, default 50.0%)',
  'PRIMER_INTERNAL_OLIGO_MIN_TM'=>'(float, default 57.0 degrees C)',
  'PRIMER_INTERNAL_OLIGO_MAX_TM'=>'(float, default 63.0 degrees C)',
  'PRIMER_INTERNAL_OLIGO_MIN_GC'=>'(float, default 20.0%)',
  'PRIMER_INTERNAL_OLIGO_MAX_GC'=>'(float, default 80.0%)',
  'PRIMER_INTERNAL_OLIGO_SALT_CONC'=>'(float, default 50.0 mM)',
  'PRIMER_INTERNAL_OLIGO_DNA_CONC'=>'(float, default 50.0 nM)',
  'PRIMER_INTERNAL_OLIGO_SELF_ANY'=>'(decimal 9999.99, default 12.00)',
  'PRIMER_INTERNAL_OLIGO_MAX_POLY_X'=>'(int, default 5)',
  'PRIMER_INTERNAL_OLIGO_SELF_END'=>'(decimal 9999.99, default 12.00)',
  'PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY'=>'(string, optional)',
  'PRIMER_INTERNAL_OLIGO_MAX_MISHYB'=>'(decimal,9999.99, default 12.00)',
  'PRIMER_INTERNAL_OLIGO_MIN_QUALITY'=>'(int, default 0)',
  'PRIMER_IO_WT_TM_GT'=>'(float, default 1.0)',
  'PRIMER_IO_WT_TM_LT'=>'(float, default 1.0)',
  'PRIMER_IO_WT_GC_PERCENT_GT'=>'(float, default 1.0)',
  'PRIMER_IO_WT_GC_PERCENT_LT'=>'(float, default 1.0)',
  'PRIMER_IO_WT_SIZE_LT'=>'(float, default 1.0)',
  'PRIMER_IO_WT_SIZE_GT'=>'(float, default 1.0)',
  'PRIMER_IO_WT_COMPL_ANY'=>'(float, default 0.0)',
  'PRIMER_IO_WT_COMPL_END'=>'(float, default 0.0)',
  'PRIMER_IO_WT_NUM_NS'=>'(float, default 0.0)',
  'PRIMER_IO_WT_REP_SIM'=>'(float, default 0.0)',
  'PRIMER_IO_WT_SEQ_QUAL'=>'(float, default 0.0)',
  'PRIMER_IO_WT_END_QUAL'=>'(float, default 0.0)',
  'PRIMER_INSIDE_PENALTY' =>  '(float, default -1.0)',
  'PRIMER_INTERNAL_OLIGO_MAX_TEMPLATE_MISHYB' => '(decimal 9999.99, default 12.00)',
  'PRIMER_OUTSIDE_PENALTY' => '(float, default 0.0)',
  'PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS' => '(boolean, default 1)',
  'PRIMER_MAX_TEMPLATE_MISPRIMING' => '(decimal,9999.99, default -1.00)',
  'PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING' => '(decimal,9999.99, default -1.00)',
  'PRIMER_PAIR_WT_TEMPLATE_MISPRIMING' => '(float, default 0.0)',
  'PRIMER_WT_TEMPLATE_MISPRIMING' => '(float, default 0.0)'
);
 $self->{'input_options'}=\%hash;
 return \%hash;