awk_wrapper.sh $input $output '$file_data' '$FS' '$OFS'value.find('\'')==-1
**What it does**
This tool runs the unix **awk** command on the selected data file.
.. class:: infomark
**TIP:** This tool uses the **extended regular** expression syntax (not the perl syntax).
**Further reading**
- Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
- Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
- Learn AWK in 1 hour (http://www.selectorweb.com/awk.html)
- awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf)
- Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt)
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**AWK programs**
Most AWK programs consist of **patterns** (i.e. rules that match lines of text) and **actions** (i.e. commands to execute when a pattern matches a line).
The basic form of AWK program is::
pattern { action 1; action 2; action 3; }
**Pattern Examples**
- **$2 == "chr3"** will match lines whose second column is the string 'chr3'
- **$5-$4>23** will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23.
- **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.)
- **$7 ~ /A{4}U/** will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.)
- **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
- If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).
**Action Examples**
- **{ print }** or **{ print $0 }** will print the entire input line (the line that matched in **pattern**). **$0** is a special marker meaning 'the entire line'.
- **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
- **{ print $4, $5-$4 }** will print the fourth column and the difference between the fifth and fourth column. (If the fourth column was start-position in the input file, and the fifth column was end-position - the output file will contain the start-position, and the length).
- If no action part is specified (not even the curly brackets) - the default action is to print the entire line.
**AWK'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**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.