What it does

This tool performs find & replace operation on a specified file.

The pattern to find uses the extended regular expression syntax (same as running 'sed -r').

TIP: If you need more complex patterns, use the sed tool.

Examples of Find Patterns

• HELLO The word 'HELLO' (case sensitive).
• AG.T The letters A,G followed by any single character, followed by the letter T.
• A{4,} Four or more consecutive A's.
• chr2[012]\t The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
• hsa-mir-([^ ]+) The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with 1 in the replace pattern.

Examples of Replace Patterns

• WORLD The word 'WORLD' will be placed whereever the find pattern was found.
• FOO-&-BAR Each time the find pattern is found, it will be surrounded with 'FOO-' at the beginning and '-BAR' at the end. & (ampersand) represents the matched find pattern.
• \1 The text which matched the first parenthesis in the Find Pattern.

Example 1

Find Pattern: HELLO Replace Pattern: WORLD

Every time the word HELLO is found, it will be replaced with the word WORLD.

Example 2

Find Pattern: ^(.{4}) Replace Pattern: &\t

Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns.

Extended Regular Expression Syntax

The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.

• ( ) { } [ ] . * ? + ^ $ are all special characters. \ can be used to "escape" a special character, allowing that special character to be searched for.
• ^ matches the beginning of a string(but not an internal line).
• ( .. ) groups a particular pattern.
• { n or n, or n,m } specifies an expected number of repetitions of the preceding pattern.
  • {n} The preceding item is matched exactly n times.
  • {n,} The preceding item ismatched n or more times.
  • {n,m} The preceding item is matched at least n times but not more than m times.
• [ ... ] creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as a-z.
• . Matches any single character except a newline.
• * The preceding item will be matched zero or more times.
• ? The preceding item is optional and matched at most once.
• + The preceding item will be matched one or more times.
• ^ has two meaning: - matches the beginning of a line or string. - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
• $ matches the end of a line or string.
• | Separates alternate possibilities.

Note: SED uses extended regular expression syntax, not Perl syntax. \d, \w, \s etc. are not supported.