What it does
This tool runs the unix grep command on the selected data file.
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
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.