# SOURCE field (XXX not in
# http://www.ncbi.nlm.nih.gov/collab/FT/index.html )
"usedin", # Indicates that feature is used in a compound
# feature in another entry
"variety", # Variety from which sequence was obtained
"virion", # Viral genomic sequence as it is encapsidated
# (distinguished from its proviral form integrated
# in a host cell's chromosome)
)
feature_qualifiers = map(Martel.Str, feature_qualifier_names)
# qualifiers escape quotes using double quotes
quote = Martel.Str('"')
quoted_chars = Std.feature_qualifier_description(Martel.Re(r'([^"\R]|"")*'))
quoted_string = (quote + quoted_chars +
Martel.Rep(Martel.AnyEol() + qualifier_space + quoted_chars) +
quote + Martel.AnyEol())
unquoted_string = Martel.AssertNot(quote) + \
Std.feature_qualifier_description(Martel.UntilEol()) + \
Martel.AnyEol()
qualifier = Std.feature_qualifier(
qualifier_space +
Martel.Str("/") +
Std.feature_qualifier_name(Martel.Alt(*feature_qualifiers)) +
(Martel.AnyEol() | # '/pseudo'
(Martel.Str("=") +
## FH - feature table header (0 or 2 per entry)
FH_block = Martel.Str("FH Key Location/Qualifiers") + \
Martel.AnyEol() + \
Martel.Str("FH") + \
Martel.AnyEol()
## FT - feature table data (>=0 per entry)
##FT_line = Martel.Str("FT ") + \
## Martel.ToEol("ft_data")
##FT_block = Martel.Rep1(FT_line)
fq_dbxref = Std.feature_qualifier_name(Martel.Str("db_xref")) + \
Martel.Str('=') + \
Std.feature_qualifier_description(
Martel.Str('"') + \
Std.dbxref(Std.dbxref_dbname(Martel.UntilSep(None, ":")) + \
Martel.Str(":") + \
Std.dbxref_dbid(Martel.UntilSep(None, '"'))) + \
Martel.Str('"')) + \
Martel.AnyEol()
fq_generic = \
Martel.Assert(Martel.Word() + Martel.Str("=")) + \
Std.feature_qualifier_name(Martel.Word()) + \
Martel.Str("=") + \
Std.feature_qualifier_description(Martel.UntilEol()) + \
Martel.AnyEol() + \
Martel.Rep(
Martel.Str("FT ") + \
(Martel.AssertNot(Martel.Str("/")) |
Martel.AssertNot(Martel.Re(r"/\w+="))) + \
