Python Std.feature_qualifier_name示例

## DR - database cross-reference   (>=0 per entry)
DR_block = sprot38.DR_block

## 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()) + \

示例#2

显示文件

# 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("=") +
      (unquoted_string |  #  '/evidence=experimental'
       quoted_string)))   #  '/translation="AAAAAAAA....
                          #   AAAAAAAAAAAAAAAAAAAA'
    )
feature = Std.feature(feature_key_line +
                      Martel.Rep(qualifier))

feature_block = Std.feature_block(
    features_line + \
    Martel.Rep1(feature),
    {"location-style": "genbank"}
    )

示例#3

显示文件

文件： genbank.py 项目： dbmi-pitt/DIKB-Evidence-analytics

# 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.Word("feature_qualifier_name")) +
    (Martel.AnyEol() | #  '/pseudo'
     (Martel.Str("=") +
     Martel.Group("feature_qualifier_description",
      (unquoted_string |  #  '/evidence=experimental'
       quoted_string))))   #  '/translation="AAAAAAAA....
                          #   AAAAAAAAAAAAAAAAAAAA'
    )

feature = Std.feature(feature_key_line +
                      Martel.Rep(qualifier))

feature_block = Std.feature_block(Martel.Rep1(feature),
                            {"location-style" : "genbank"})

# BASE COUNT    28300 a  15069 c  15360 g  27707 t