grep_wrapper.sh $input $output '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive Match Don't Match value.find('\'')==-1 case insensitive case sensitive text file (for further processing) Highlighted HTML (for easier viewing)

**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) ----- **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). ----- **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.