Std.feature_qualifier_description(Martel.UntilEol()) + \
Martel.AnyEol() + \
Martel.Rep(
Martel.Str("FT ") + \
(Martel.AssertNot(Martel.Str("/")) |
Martel.AssertNot(Martel.Re(r"/\w+="))) + \
Std.feature_qualifier_description(Martel.UntilEol()) + \
Martel.AnyEol())
feature_qualifier = Std.feature_qualifier(
Martel.Str("FT /") + \
(fq_dbxref | fq_generic))
feature = Std.feature(
Martel.Str("FT ") + \
Std.feature_name(Martel.UntilSep(sep = " ")) + \
whitespace + \
Std.feature_location(Martel.UntilEol()) + \
Martel.AnyEol() + \
Martel.Rep(Martel.Str("FT ") + \
Martel.AssertNot(Martel.Str("/")) + \
Std.feature_location(Martel.UntilEol()) + \
Martel.AnyEol()
) + \
Martel.Rep(feature_qualifier)
)
FT_block = Std.feature_block(Martel.Rep(feature),
{"location-style": "genbank"})
feature_key = Martel.Group("feature_key",
Martel.Alt(*valid_feature_keys))
location = Martel.Group("location",
Std.feature_location(Martel.UntilEol()) +
Martel.AnyEol() +
Martel.Rep(qualifier_space +
Martel.AssertNot(Martel.Str("/")) +
Std.feature_location(Martel.UntilEol()) +
Martel.AnyEol())
)
feature_key_line = Martel.Group("feature_key_line",
big_indent_space +
Std.feature_name(feature_key) +
Martel.Spaces() +
location)
# -- now set up all of the info we can have for qualifiers
# a listing of valid qualifier keys
# For now use a simple list and get all of the matching text.
# In the future could allow more specific matches for each key.
# XXX Because of a bug in Martel, if one name is a substring of
# XXX another, put the longer name first. Eg, "clone_lib" before "clone"
feature_qualifier_names = (
"allele", # Name of the allele for the a given gene
"anticodon", # Location of the anticodon of tRNA and the amino
# acid for which it codes
"bound_moiety", # Moiety bound
"cell_line", # Cell line from which the sequence was obtained
# "FT " + ".{8}" + " " + ".{6}" + " " + ".{6}" + " " + "[^\R]*" + "\R"
# "FT .{8} .{6} .{6} [^\R]*\R"
##FT_range = Martel.Group("FT",
## Martel.Re("FT (?P<ft_name>.{8}) " \
## "(?P<ft_from>.{6}) (?P<ft_to>.{6})" \
## "( (?P<ft_description>[^\R]*))?\R")
## )
##FT_continuation = Martel.Group("FT_continuation",
## Martel.Re("FT " \
## "(?P<ft_description>[^\R]*)\R")
## )
##FT = Martel.Group("feature", FT_range + Martel.Rep(FT_continuation))
FT_name = Std.feature_name(Martel.Re(r".{8}"))
FT_start = Std.feature_location_start(Martel.Re(r".{6}"))
FT_end = Std.feature_location_end(Martel.Re(r".{6}"))
FT_desc = Std.feature_description(Martel.UntilEol())
FT_range = Martel.Str("FT ") + \
FT_name + \
Martel.Str(" ") + \
FT_start + \
Martel.Str(" ") + \
FT_end + \
Martel.Opt(Martel.Str(" ") + \
FT_desc) + \
Martel.AnyEol()
FT_continuation = Martel.Str("FT ") + \