Martel.ToEol(block_data) +
Martel.Rep(Martel.AnyEol() |
(Martel.Str(" " * INDENT) + Martel.ToEol(block_data))))
# The first line
# LOCUS AC007323 86436 bp DNA PLN 19-JAN-2000
locus = Std.dbid(Martel.Word(), {"dbname": "gb", "type": "primary"})
size = Martel.Group("size",
Martel.Rep1(Martel.Integer()))
# deal with the different kinds of residues we can have
residue_prefixes = Martel.Str("ss-", "ds-", "ms-")
residue_types = [
Std.alphabet(Martel.Str("DNA"), {"alphabet": "iupac-ambiguous-dna"}),
Std.alphabet(Martel.Str("RNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("mRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("tRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("rRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("uRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("snRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("PROTEIN"), {"alphabet": "iupac-protein"}),
]
residue_type = Martel.Group("residue_type",
Martel.Opt(Martel.Alt(residue_prefixes)) +
Martel.Opt(Martel.Alt(*residue_types)) +
Martel.Opt(Martel.Opt(blank_space) +
Martel.Str("circular", "linear")))
## ID - identification (begins each entry; 1 per entry)
# ID entryname dataclass; molecule; division; sequencelength BP.
divisions = Martel.Re("EST|PHG|FUN|GSS|HTC|HTG|HUM|INV|ORG|MAM|VRT|PLN|" + \
"PRO|ROD|SYN|STS|UNC|VRL|[A-Z]{3}")
# XXX is found in S40706
ID_line = Martel.Str("ID ") + \
Std.dbid(Martel.UntilSep("entry_name", " "), {"type": "primary",
"dbname": "embl"}) + \
whitespace + \
Martel.ToSep("dataclass", ";") + \
whitespace + \
Martel.Group("molecule",
Std.alphabet(Martel.Str("DNA", "circular DNA"),
{"alphabet": "iupac-ambiguous-dna"}) |
Std.alphabet(Martel.Str("RNA", "circular RNA"),
{"alphabet": "iupac-ambiguous-rna"}) |
Std.alphabet(Martel.Str("XXX"),
{"alphabet": "nucleotide"})) + \
Martel.Str("; ") + \
Martel.Group("division", divisions) + \
Martel.Str("; ") + \
Martel.Digits("length") + \
Martel.Str(" BP.") + \
Martel.AnyEol()
## AC - accession number (>=1 per entry)
accession = Std.dbid(Martel.UntilSep("accession", ";"),
{"type": "accession",
