Module: Bio::GFF::GFF2::Escape

Included in:: Record, Record::Value

Defined in:: lib/bio/db/gff.rb

Overview

Private methods for GFF2 escaping characters. Internal only. Users should not use this module directly.

Constant Summary collapse

UNSAFE_GFF2 = unsafe characters to be escaped

/[^-_.!~*'()a-zA-Z\d\/?:@+$\[\] \x80-\xfd><;=,%^&\|`]/n

IDENTIFIER_GFF2 = GFF2 standard identifier

/\A[A-Za-z][A-Za-z0-9_]*\z/n

NUMERIC_GFF2 = GFF2 numeric value

/\A[-+]?([0-9]+|[0-9]*\.[0-9]*)([eE][+-]?[0-9]+)?\z/n

BACKSLASH = List of 1-letter special backslash code. The letters other than listed here are the same as those of without backslash, except for “x” and digits. (Note that u (unicode) is not supported.)

{
  't'  => "\t",
  'n'  => "\n",
  'r'  => "\r",
  'f'  => "\f",
  'b'  => "\b",
  'a'  => "\a",
  'e'  => "\e",
  'v'  => "\v",
  # 's'  => " ",
}.freeze

CHAR2BACKSLASH = inverted hash of BACKSLASH

BACKSLASH.invert.freeze

CHAR2BACKSLASH_EXTENDED = inverted hash of BACKSLASH, including double quote and backslash

CHAR2BACKSLASH.merge({ '"' => '"', "\\" => "\\" }).freeze

PROHIBITED_GFF2_COLUMNS = prohibited characters in GFF2 columns

/[\t\r\n\x00-\x08\x0b\x0c\x0e-\x1f\x7f\xfe\xff]/

PROHIBITED_GFF2_TAGS = prohibited characters in GFF2 attribute tags

/[\s\"\;\x00-\x08\x0e-\x1f\x7f\xfe\xff]/