What it does

This tool runs the unix sed command on the selected data file.

TIP: This tool uses the extended regular expression syntax (same as running 'sed -r').

Further reading

• Short sed tutorial (http://www.linuxhowtos.org/System/sed_tutorial.htm)
• Long sed tutorial (http://www.grymoire.com/Unix/Sed.html)
• sed faq with good examples (http://sed.sourceforge.net/sedfaq.html)
• sed cheat-sheet (http://www.catonmat.net/download/sed.stream.editor.cheat.sheet.pdf)

Sed commands

The most useful sed command is s (substitute).

Examples

• s/hsa// will remove the first instance of 'hsa' in every line.
• s/hsa//g will remove all instances (beacuse of the g) of 'hsa' in every line.
• s/A{4,}/--&--/g will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The & marker is a place holder for 'whatever matched the regular expression'.
• s/hsa-mir-([^ ]+)/short name: \1 full name: &/ will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'. The \1 marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's $1) .

sed's 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.