Regular Expressions

Mon, 01 Jan 0001 00:00:00 +0000

Regular Expressions #

Regular expressions are a powerful tool for describing patterns in text. They are used in several OBITools like obigrep , obiannotate or obiscript .

Single characters #

Pattern	Description
`.`	any character, possibly including newline (flag s=true)
`[xyz]`	character class
`[^xyz]`	negated character class
`[[:alpha:]]`	ASCII character class
`[[:^alpha:]]`	negated ASCII character class

Composites #

Pattern	Description
`xy`	x followed by y
`x\|y`	x or y (prefer x)

Repetitions #

Pattern	Description
`x*`	zero or more x, prefer more
`x+`	one or more x, prefer more
`x?`	zero or one x, prefer one
`x{n,m}`	n or n+1 or … or m x, prefer more
`x{n,}`	n or more x, prefer more
`x{n}`	exactly n x
`x*?`	zero or more x, prefer fewer
`x+?`	one or more x, prefer fewer
`x??`	zero or one x, prefer zero
`x{n,m}?`	n or n+1 or … or m x, prefer fewer
`x{n,}?`	n or more x, prefer fewer
`x{n}?`	exactly n x

Grouping #

Pattern	Description
`(re)`	numbered capturing group (submatch)
`(?P<name>re)`	named & numbered capturing group (submatch)
`(?<name>re)`	named & numbered capturing group (submatch)
`(?:re)`	non-capturing group
`(?flags)`	set flags within current group; non-capturing
`(?flags:re)`	set flags during re; non-capturing

Character classes #

Pattern	Description
`[\d]`	digits (== \d)
`[^\d]`	not digits (== \D)
`[\D]`	not digits (== \D)
`[^\D]`	not not digits (== \d)
`[[:name:]]`	named ASCII class inside character class (== [:name:])
`[^[:name:]]`	named ASCII class inside negated character class (== [:^name:])
`[\p{Name}]`	named Unicode property inside character class (== \p{Name})
`[^\p{Name}]`	named Unicode property inside negated character class (== \P{Name})

Named character classes #

Pattern	Description
`[[:alnum:]]`	alphanumeric (== `[0-9A-Za-z]`)
`[[:alpha:]]`	alphabetic (== `[A-Za-z]`)
`[[:ascii:]]`	ASCII (== `[\x00-\x7F]`)
`[[:blank:]]`	blank (== `[\t ]`)
`[[:cntrl:]]`	control (== `[\x00-\x1F\x7F]`)
`[[:digit:]]`	digits (== `[0-9]`)
`[[:graph:]]`	graphical (== `[!-~]` == [A-Za-z0-9!"#$%&'()*+,\-./:;<=>?@[\\\]^_`{\|}~])
`[[:lower:]]`	lower case (== `[a-z]`)
`[[:print:]]`	printable (== `[ -~]` == `[[:graph:]]`)
`[[:punct:]]`	punctuation (== [!-/:-@[-\`{-~])
`[[:space:]]`	whitespace (== `[\t\n\v\f\r ]`)
`[[:upper:]]`	upper case (== `[A-Z]`)
`[[:word:]]`	word characters (== `[0-9A-Za-z_]`)
`[[:xdigit:]]`	hex digit (== `[0-9A-Fa-f]`)

DNA Patterns

Mon, 01 Jan 0001 00:00:00 +0000

DNA Patterns #

DNA patterns are useful for describing short DNA sequences like oligonucleotides. They are used by several OBITools like obimultiplex , obipcr or obigrep . The advantage of using DNA patterns over classical regular expressions is that they can be matched with errors. Allowed errors can be simple mismatches, or mismatches and insertions/deletions.

Patterns on OBITools4 documentation

Regular Expressions

Regular Expressions #

Single characters #

Composites #

Repetitions #

Grouping #

Character classes #

Named character classes #

DNA Patterns

DNA Patterns #