grep_wrapper.sh $input $output '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitivevalue.find('\'')==-1
**What it does**
This tool runs the unix **grep** command on the selected data file.
.. class:: infomark
**TIP:** This tool uses the **perl** regular expression syntax (same as running 'grep -P'). This is **NOT** the POSIX or POSIX-extended syntax (unlike the awk/sed tools).
**Further reading**
- Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
- Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf)
- Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)
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**Grep Examples**
- **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**)
- **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC
- **TTT.{4,10}AAA** would match lines with 3 Ts, followed by 4 to 10 characters (any characeters), followed by 3 As.
- **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file.
- **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
- **hsa|mmu** would match lines containing "hsa" or "mmu" (or both).
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**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.
- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- **^** matches the beginning of a string(but not an internal line).
- **\\d** matches a digit, same as [0-9].
- **\\D** matches a non-digit.
- **\\s** matches a whitespace character.
- **\\S** matches anything BUT a whitespace.
- **\\t** matches a tab.
- **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
- **\\W** matches anything but an alphanumeric character.
- **(** .. **)** groups a particular pattern.
- **\\Z** matches the end of a string(but not a internal line).
- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
- **{n}** The preceding item is matched exactly n times.
- **{n,}** The preceding item ismatched n or more times.
- **{n,m}** The preceding item is matched at least n times but not more than m times.
- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
- **.** Matches any single character except a newline.
- ***** The preceding item will be matched zero or more times.
- **?** The preceding item is optional and matched at most once.
- **+** The preceding item will be matched one or more times.
- **^** has two meaning:
- matches the beginning of a line or string.
- indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
- **$** matches the end of a line or string.
- **\|** Separates alternate possibilities.