Examples of expressions you may find useful regarding paired end naming specifications follow. Please note this is not a complete list of regular expressions, and the definitions of the terms used are limited to their application to SeqMan NGen paired end naming specifications.
| Special Characters | |
|---|---|
| [ ] | Character class used to enclose a list of alternatives. For example: [Aa]bc matches abc and Abc. If the first character is a carat (^), it means anything but the characters on the list. Thus: [^a]bc matches xbc but not abc. |
| \ | A switch that makes special characters literal and literal characters special. |
| ( ) | Grouping--used to delimit a string comprising a “phrase.” Phrases are necessary in paired end specification so you can match a pair of forward and reverse reads while still distinguishing their orientation. In SeqMan NGen, phrases in parentheses must match for two reads to qualify as a pair; phrases outside the parentheses are used to distinguish members of the same pair. |
| \d | Any digit (0-9) |
| \D | Any non-digit character. |
| \w | Any alphanumeric “word” character (including “_”) |
| . | Any character |
| | | Alternate--either the term before “|” or after “|” |
| ^ | Match at the beginning of the line only. |
| $ | Match at the end of the line only. |
| Numerical Modifiers | |
| * | 0 or more |
| + | 1 or more |
| ? | 1 or 0 |
| {n} | Exactly n |
| {n,} | At least n |
| {n,m} | At least n but not more than m |
| Example Expressions and Their Meanings | |
| d | Literally the letter d |
| \d | Any digit (0-9) |
| \d* | Zero or more digits |
| \d+ | One or more digits |
| (\d+) | A phrase comprising one or more digits--same as “\d+”, but causes SeqMan NGen to match the names from the string inside the phrase when other characters in the name may not match. |
| \. | Literally the period symbol (.) |
| . | Any character |
| .+ | One or more of any characters |
| .* | Zero or more of any characters |
| a|b | a OR b |
| ab[i1] | abi or ab1 |
| abi$ | Ends with abi |
| [\.\d] | A period OR a digit |
| [abc] | a OR b OR c |
| [abc]+ | One or more characters from the set a, b, c |
| .*f | Any number of any characters followed by the letter “f” |
| (.*)f* | A phrase comprising any number of any characters, followed by the letter “f”--same as “.*f”, but causes SeqMan NGen to match the phrase in parentheses without matching the “f” in a read name |
| (\D+)r(\d+) | One or more non-digit characters followed by “r” followed by one or more digits. |
| (\d{2,4})f(\.abi) | Two, three or four digits followed by “f” followed by “.abi” |
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