Package Bio :: Package Emboss :: Module primer3_format
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Module primer3_format

source code

Martel definitions for the output files produced by primer3.

Variables [hide private]
  any_space = Martel.Re("[ ]+")
  blank_line = Martel.AnyEol()
  comment_line = Martel.Str("#")+ Martel.ToEol()
  comments = Martel.Group("comments", blank_line+ comment_line+ ...
  product_size = Martel.Group("product_size", Martel.Re("[\d]+"))
  start_primer = Martel.Group("start_primer", any_space+ Martel....
  primer_start_line = Martel.Group("primer_start_line", start_pr...
  single_primer_line = Martel.Group("single_primer_line", blank_...
  primer_space = Martel.Str(" "* 5)
  any_integer = Martel.Re("[\d]+")
  any_float = Martel.Re("[\d\.]+")
  sequence = Martel.Re("[GATCN]+")
  forward_primer_start = Martel.Group("forward_start", any_integer)
  forward_primer_length = Martel.Group("forward_length", any_int...
  forward_primer_tm = Martel.Group("forward_tm", any_float)
  forward_primer_gc = Martel.Group("forward_gc", any_float)
  forward_primer_seq = Martel.Group("forward_seq", sequence)
  forward_line = Martel.Group("forward_line", primer_space+ Mart...
  reverse_primer_start = Martel.Group("reverse_start", any_integer)
  reverse_primer_length = Martel.Group("reverse_length", any_int...
  reverse_primer_tm = Martel.Group("reverse_tm", any_float)
  reverse_primer_gc = Martel.Group("reverse_gc", any_float)
  reverse_primer_seq = Martel.Group("reverse_seq", sequence)
  reverse_line = Martel.Group("reverse_line", primer_space+ Mart...
  internal_oligo_start = Martel.Group("internal_start", any_inte...
  internal_oligo_length = Martel.Group("internal_length", any_in...
  internal_oligo_tm = Martel.Group("internal_tm", any_float)
  internal_oligo_gc = Martel.Group("internal_gc", any_float)
  internal_oligo_seq = Martel.Group("internal_seq", sequence)
  internal_line = Martel.Group("internal_line", primer_space+ Ma...
  record = Martel.Group("primer3_record", comments+ Martel.Alt(M...
Variables Details [hide private]

comments

Value:
Martel.Group("comments", blank_line+ comment_line+ blank_line+ comment\
_line)

start_primer

Value:
Martel.Group("start_primer", any_space+ Martel.Re("[\d]+")+ Martel.Str\
(" PRODUCT SIZE: "))

primer_start_line

Value:
Martel.Group("primer_start_line", start_primer+ product_size+ Martel.A\
nyEol())

single_primer_line

Value:
Martel.Group("single_primer_line", blank_line)

forward_primer_length

Value:
Martel.Group("forward_length", any_integer)

forward_line

Value:
Martel.Group("forward_line", primer_space+ Martel.Str("FORWARD PRIMER"\
)+ any_space+ forward_primer_start+ any_space+ forward_primer_length+ \
any_space+ forward_primer_tm+ any_space+ forward_primer_gc+ any_space+\
 forward_primer_seq+ Martel.AnyEol())

reverse_primer_length

Value:
Martel.Group("reverse_length", any_integer)

reverse_line

Value:
Martel.Group("reverse_line", primer_space+ Martel.Str("REVERSE PRIMER"\
)+ any_space+ reverse_primer_start+ any_space+ reverse_primer_length+ \
any_space+ reverse_primer_tm+ any_space+ reverse_primer_gc+ any_space+\
 reverse_primer_seq+ Martel.AnyEol())

internal_oligo_start

Value:
Martel.Group("internal_start", any_integer)

internal_oligo_length

Value:
Martel.Group("internal_length", any_integer)

internal_line

Value:
Martel.Group("internal_line", primer_space+ Martel.Str("INTERNAL OLIGO\
")+ any_space+ internal_oligo_start+ any_space+ internal_oligo_length+\
 any_space+ internal_oligo_tm+ any_space+ internal_oligo_gc+ any_space\
+ internal_oligo_seq+ Martel.AnyEol())

record

Value:
Martel.Group("primer3_record", comments+ Martel.Alt(Martel.Str("\n"* 3\
)+ Martel.Opt(Martel.Str("\n"* 4)), Martel.Rep(Martel.Alt(blank_line+ \
primer_start_line, single_primer_line)+ Martel.Alt(forward_line+ blank\
_line+ reverse_line+ blank_line, reverse_line+ blank_line, forward_lin\
e+ blank_line, internal_line+ blank_line))+ blank_line+ blank_line+ Ma\
rtel.Rep(blank_line)))