lines that match an expression grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert Matching NOT Matching

.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* ----- **Syntax** The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern describing a certain amount of text. - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. - **\\A** matches the beginning of a string(but not an internal line). - **\\d** matches a digit, same as [0-9]. - **\\D** matches a non-digit. - **\\s** matches a whitespace character. - **\\S** matches anything BUT a whitespace. - **\\t** matches a tab. - **\\w** matches an alphanumeric character. - **\\W** matches anything but an alphanumeric character. - **(** .. **)** groups a particular pattern. - **\\Z** matches the end of a string(but not a internal line). - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. - **{n}** The preceding item is matched exactly n times. - **{n,}** The preceding item is matched n or more times. - **{n,m}** The preceding item is matched at least n times but not more than m times. - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. - **.** Matches any single character except a newline. - ***** The preceding item will be matched zero or more times. - **?** The preceding item is optional and matched at most once. - **+** The preceding item will be matched one or more times. - **^** has two meaning: - matches the beginning of a line or string. - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. - **$** matches the end of a line or string. - **\|** Separates alternate possibilities. ----- **Example** - **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file. - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively. - **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly separated with commas such as 23,078,651. - **(abc)|(def)** would match either "abc" or "def". - **^\\W+#** would match any line that is a comment.