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 + 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())
# XXX This record definition is ugly. But it works :-)
record = Martel.Group("primer3_record",
comments + \
Martel.Alt(
# case 1. primer file with nothing
Martel.Str("\n" * 3) +
Martel.Opt(Martel.Str("\n" * 4)),
# case 2. some primers have been picked
Martel.Rep(
# case 2a. we are designing a primer pair
Martel.Alt(blank_line + primer_start_line,
# case 2b. we are designing a single primer
single_primer_line) +
# case 2a. both primer pairs
Martel.Alt(forward_line + blank_line +
reverse_line + blank_line,
# case 2b1. Reverse primer
reverse_line + blank_line,
# case 2b2, Forward primer
forward_line + blank_line,
# case 2b3, Internal oligo
internal_line + blank_line)) +
# 0 or more
RT = Simple("RT", "reference_title")
RT_block = Martel.Group("RT_block", Martel.Rep1(RT))
#--- RL
# 1 or more
RL = Simple("RL", "reference_location")
RL_block = Martel.Group("RL_block", Martel.Rep1(RL))
reference = Martel.Group("reference",
RN + \
RP + \
Martel.Opt(RC_block) + \
Martel.Opt(RX) + \
RA_block + \
Martel.Opt(RT_block) + \
RL_block
)
############
#--- CC
CC_begin = Martel.Group("CC",
Martel.Re("CC -!- ") + \
Martel.ToEol("comment_text"))
CC = Martel.Group("CC",
Martel.Re("CC ") + \