Python Std.feature_qualifier示例

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+="))) + \
           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)
    )

示例#2

显示文件

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"}
    )


# BASE COUNT    28300 a  15069 c  15360 g  27707 t

示例#3

显示文件

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

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
base_count = Martel.Group("base_count",
                          Martel.Re("[\w\d ]+"))