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)))
"(?P<primary_identifier>[^;]+); " \
"(?P<secondary_identifier>([^.\R]|(?!.\R)\.)+)")
DR_prosite = Martel.Re("(?P<database_identifier>(PROSITE|PFAM)); " \
"(?P<primary_identifier>[^;]+); " \
"(?P<secondary_identifier>[^;]+); " \
"(?P<status_identifier>[^.]+)")
DR_embl = Martel.Re("(?P<database_identifier>EMBL); " \
"(?P<primary_identifier>[^;]+); " \
"(?P<secondary_identifier>[^;]+); " \
"(?P<status_identifier>[^.]+)")
DR = Martel.Group("DR", Martel.Str("DR ") + \
Martel.Group("database_reference",
Martel.Alt(DR_embl, DR_prosite, DR_general)) + \
Martel.Str(".") + Martel.AnyEol())
DR_block = Martel.Group("DR_block", Martel.Rep1(DR))
#--- KW
KW = Simple("KW", "keyword")
KW_block = Martel.Group("KW_block", Martel.Rep1(KW))
#--- FT
# FT DOMAIN 77 88 ASP/GLU-RICH (ACIDIC).
# 123456789012345678901234567890123456789012345678901234567890123456789012345
# 1 2 3 4 5 6 7
# FT ........ ...... ...... .........................................
