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"""Martel definitions for the output files produced by primer3.
"""
import Martel
any_space = Martel.Re("[ ]+")
blank_line = Martel.AnyEol()
comment_line = Martel.Str("#") + Martel.ToEol()
# comments and blank lines in the file
comments = Martel.Group("comments",
blank_line +
comment_line +
blank_line +
comment_line)
# 1 PRODUCT SIZE: 289
product_size = Martel.Group("product_size",
Martel.Re("[\d]+"))
start_primer = Martel.Group("start_primer",
any_space + Martel.Re("[\d]+") +
Martel.Str(" PRODUCT SIZE: "))
primer_start_line = Martel.Group("primer_start_line",
start_primer +
product_size + Martel.AnyEol())
# a blank line that signifies a new primer is coming up
single_primer_line = Martel.Group("single_primer_line",
blank_line)
# FORWARD PRIMER 1725 20 59.96 55.00 AGGGAAGGGATGCTAGGTGT
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_integer)
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 + 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 1994 20 59.99 55.00 AGAAGCACACCTCTCCCTGA
reverse_primer_start = Martel.Group("reverse_start",
any_integer)
reverse_primer_length = Martel.Group("reverse_length",
any_integer)
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 + 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 197 20 59.96 40.00 AATTGCACATAACGGATGCA
internal_oligo_start = Martel.Group("internal_start",
any_integer)
internal_oligo_length = Martel.Group("internal_length",
any_integer)
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)) +
blank_line + blank_line + Martel.Rep(blank_line)))
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