| dreg

## Function

Regular expression search of nucleotide sequence(s)

## Description

dreg searches one or more sequences with the supplied regular expression and writes an output file with the matches.

## Usage

Here is a sample session with dreg

    % dreg
    Regular expression search of nucleotide sequence(s)
    Input nucleotide sequence(s): tembl:x13776
    Regular expression pattern: ggtacc
    Output report [x13776.dreg]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                      format, or reference (input USA)
      [-pattern]           regexp     Any regular expression pattern is accepted)
      [-outfile]           report     [*.dreg] Output report file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-pattern" associated qualifiers
       -pformat2           string     File format
       -pname2             string     Pattern base name

       "-outfile" associated qualifiers
       -rformat3           string     Report format
       -rname3             string     Base file name
       -rextension3        string     File name extension
       -rdirectory3        string     Output directory
       -raccshow3          boolean    Show accession number in the report
       -rdesshow3          boolean    Show description in the report
       -rscoreshow3        boolean    Show the score in the report
       -rstrandshow3       boolean    Show the nucleotide strand in the report
       -rusashow3          boolean    Show the full USA in the report
       -rmaxall3           integer    Maximum total hits to report
       -rmaxseq3           integer    Maximum hits to report for one sequence

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-pattern] (Parameter 2) | Regular expression pattern | Any regular expression pattern is accepted | Required
[-outfile] (Parameter 3) | Output report file name | Report output file | <*>.dreg
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

Any nucleic sequence.

### Input files for usage example

'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x13776

    ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
    XX
    AC   X13776; M43175;
    XX
    DT   19-APR-1989 (Rel. 19, Created)
    DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
    XX
    DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
    XX
    KW   aliphatic amidase regulator; amiC gene; amiR gene.
    XX
    OS   Pseudomonas aeruginosa
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
    OC   Pseudomonadaceae; Pseudomonas.
    XX
    RN   [1]
    RP   1167-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    RN   [2]
    RP   1167-2167
    RX   DOI; 10.1016/0014-5793(89)80249-2.
    RX   PUBMED; 2495988.
    RA   Lowe N., Rice P.M., Drew R.E.;
    RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
    RT   aeruginosa";
    RL   FEBS Lett. 246(1-2):39-43(1989).
    XX
    RN   [3]
    RP   1-1292
    RX   PUBMED; 1907262.
    RA   Wilson S., Drew R.;
    RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
    RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
    RT   product.";
    RL   J. Bacteriol. 173(16):4914-4921(1991).
    XX
    RN   [4]
    RP   1-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    DR   GOA; Q51417.
    DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
    XX

      [Part of this file has been deleted for brevity]

    FT                   /replace=""
    FT                   /note="ClaI fragment deleted in pSW36,  constitutive
    FT                   phenotype"
    FT   misc_feature    1
    FT                   /note="last base of an XhoI site"
    FT   misc_feature    648..653
    FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
    FT                   constitutive expression of amiE"
    FT   conflict        1281
    FT                   /replace="g"
    FT                   /citation=[3]
    XX
    SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
         ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
         ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
         aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
         aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
         agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
         ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
         tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
         agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
         acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
         ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
         gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
         acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
         cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
         ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
         aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
         acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
         tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
         tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
         acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
         gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
         agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
         ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
         cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
         gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
         gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
         gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
         cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
         tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
         gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
         ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
         gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
         aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
         catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
         gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
         gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
         ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
         cctcgag                                                                2167
    //

## Output file format

### Output files for usage example

### File: x13776.dreg

    ########################################
    # Program: dreg
    # Rundate: Tue 15 Jul 2008 12:00:00
    # Commandline: dreg
    #    -sequence tembl:x13776
    #    -pattern ggtacc
    # Report_format: seqtable
    # Report_file: x13776.dreg
    ########################################

    #=======================================
    #
    # Sequence: X13776     from: 1   to: 2167
    # HitCount: 1
    #
    # Pattern: ggtacc
    #
    #=======================================

      Start     End  Strand Pattern_name Sequence
          1       6       + regex1       ggtacc

    #---------------------------------------
    #---------------------------------------

    #---------------------------------------
    # Total_sequences: 1
    # Total_hitcount: 1
    #---------------------------------------

## Data files

None.

## Notes

A regular expression is a way of specifying an ambiguous pattern to search for. Regular expressions are commonly used in some computer programming languages and may be more familiar to some users than to others.

The following is a short guide to regular expressions in EMBOSS:

^
  use this at the start of a pattern to insist that the pattern can only match at the start of a sequence. (eg. '^AUG' matches a start codon at the start of the sequence)
$
  use this at the end of a pattern to insist that the pattern can only match at the end of a sequence (eg. 'A+$' matches a poly-A sequence at the end of the sequence)
()
  groups a pattern. This is commonly used with '|' (eg. '(AUG)|(ATG)' matches either the DNA or RNA form of the initiation codon )
|
  This is the OR operator to enable a match to be made to either one pattern OR another. There is no AND operator in this version of regular expressions.

The following quantifier characters specify the number of time that the character before (in this case 'x') matches:

x?
  matches 0 or 1 times (ie, '' or 'x')
x*
  matches 0 or more times (ie, '' or 'x' or 'xx' or 'xxx', etc)
x+
  matches 1 or more times (ie, 'x' or 'xx' or 'xxx', etc)

{min,max}
  Braces can enclose the specification of the minimum and maximum number of matches. A match of 'x' of between 3 and 6 times is: 'x{3,6}'

Quantifiers can follow any of the following types of character specification:

x
  any character (ie 'A')
\x
  the character after the backslash is used instead of its normal regular expression meaning. This is commonly used to turn off the special meaning of the characters '^$()|?*+[]-.'. It may be especially useful when searching for gap characters in a sequence (eg '\.' matches only a dot character '.')
[xy]
  match one of the characters 'x' or 'y'. You may have one or more characters in this set.
[x-z]
  match any one of the set of characters starting with 'x' and ending in 'y' in ASCII order (eg '[A-G]' matches any one of: 'A', 'B', 'C', 'D', 'E', 'F', 'G')
[^x-z]
  matches anything except any one of the group of characters in ASCII order (eg '[^A-G]' matches anything EXCEPT any one of: 'A', 'B', 'C', 'D', 'E', 'F', 'G')
.
  the dot character matches any other character (eg: 'A.G' matches 'AAG', 'AaG', 'AZG', 'A-G' 'A G', etc.)

Combining some of these features gives the example:

    '([AGC]+GGG)|(TTTGGG)'

which matches one or more of any one of 'A' or 'G' or 'C' followed by three 'G's or it matches just 'TTTGGG'.

Regular expressions are case-sensitive. The pattern 'AAAA' will not match the sequence 'aaaa'. For this reason, both your pattern and the input sequences are converted to upper-case.

## The syntax in detail

EMBOSS uses the publicly available PCRE code library to do regular expressions.

The full documentation of the PCRE system can be seen at http://www.pcre.org/pcre.txt

A condensed description of the syntax of PCRE follows, without features that are thought not to be required for searching for patterns in sequences (e.g. matching non-printing characters, atomic grouping, back-references, assertion, conditional sub-patterns, recursive patterns, subpatterns as subroutines, callouts). If you do neot see a required function described below, please see the full description on the PCRE web site.

### PCRE REGULAR EXPRESSION DETAILS

The syntax and semantics of the regular expressions supported by PCRE are described below. Regular expressions are also described in the Perl documentation and in a number of other books, some of which have copious examples. Jeffrey Friedl's "Mastering Regular Expressions", published by O'Reilly, covers them in great detail. The description here is intended as reference documentation.

A regular expression is a pattern that is matched against a subject string from left to right. Most characters stand for themselves in a pattern, and match the corresponding characters in the subject. As a trivial example, the pattern

The quick brown fox

matches a portion of a subject string that is identical to itself. The power of regular expressions comes from the ability to include alternatives and repetitions in the pattern. These are encoded in the pattern by the use of meta-characters, which do not stand for themselves but instead are interpreted in some special way.

There are two different sets of meta-characters: those that are recognized anywhere in the pattern except within square brackets, and those that are recognized in square brackets. Outside square brackets, the meta-characters are as follows:

           \      general escape character with several uses
           ^      assert start of string (or line, in multiline mode)
           $      assert end of string (or line, in multiline mode)
           .      match any character except newline (by default)
           [      start character class definition
           |      start of alternative branch
           (      start subpattern
           )      end subpattern
           ?      extends the meaning of (
                  also 0 or 1 quantifier
                  also quantifier minimizer
           *      0 or more quantifier
           +      1 or more quantifier
                  also "possessive quantifier"
           {      start min/max quantifier

Part of a pattern that is in square brackets is called a "character class". In a character class the only meta-characters are:

           \      general escape character
           ^      negate the class, but only if the first character
           -      indicates character range
           [      POSIX character class (only if followed by POSIX
                    syntax)
           ]      terminates the character class

The following sections describe the use of each of the meta-characters.

#### BACKSLASH

The backslash character has several uses. Firstly, if it is followed by a non-alphameric character, it takes away any special meaning that character may have. This use of backslash as an escape character applies both inside and outside character classes.

For example, if you want to match a * character, you write \* in the pattern. This escaping action applies whether or not the following character would otherwise be interpreted as a meta-character, so it is always safe to precede a nonalphameric with backslash to specify that it stands for itself. In particular, if you want to match a backslash, you write \\.

The third use of backslash is for specifying generic character types:

           \d     any decimal digit
           \D     any character that is not a decimal digit
           \s     any whitespace character
           \S     any character that is not a whitespace character
           \w     any "word" character
           W     any "non-word" character

Each pair of escape sequences partitions the complete set of characters into two disjoint sets. Any given character matches one, and only one, of each pair.

A "word" character is any letter or digit or the underscore character, that is, any character which can be part of a Perl "word". The definition of letters and digits is controlled by PCRE's character tables, and may vary if locale- specific matching is taking place (see "Locale support" in the pcreapi page). For example, in the "fr" (French) locale, some character codes greater than 128 are used for accented letters, and these are matched by \w.

These character type sequences can appear both inside and outside character classes. They each match one character of the appropriate type. If the current matching point is at the end of the subject string, all of them fail, since there is no character to match.

The fourth use of backslash is for certain simple assertions. An assertion specifies a condition that has to be met at a particular point in a match, without consuming any characters from the subject string. The use of subpatterns for more complicated assertions is described below. The backslashed assertions are

           \b     matches at a word boundary
           \B     matches when not at a word boundary
           \A     matches at start of subject
           \Z     matches at end of subject or before newline at end
           \z     matches at end of subject
           \G     matches at first matching position in subject

These assertions may not appear in character classes (but note that \b has a different meaning, namely the backspace character, inside a character class).

A word boundary is a position in the subject string where the current character and the previous character do not both match \w or \W (i.e. one matches \w and the other matches \W), or the start or end of the string if the first or last character matches \w, respectively. The \A, \Z, and \z assertions differ from the traditional circumflex and dollar (described below) in that they only ever match at the very start and end of the subject string, whatever options are set. Thus, they are independent of multiline mode.

#### CIRCUMFLEX AND DOLLAR

Outside a character class, in the default matching mode, the circumflex character is an assertion which is true only if the current matching point is at the start of the subject string. Inside a character class, circumflex has an entirely different meaning (see below).

Circumflex need not be the first character of the pattern if a number of alternatives are involved, but it should be the first thing in each alternative in which it appears if the pattern is ever to match that branch. If all possible alternatives start with a circumflex, that is, if the pattern is constrained to match only at the start of the subject, it is said to be an "anchored" pattern. (There are also other constructs that can cause a pattern to be anchored.)

A dollar character is an assertion which is true only if the current matching point is at the end of the subject string, or immediately before a newline character that is the last character in the string (by default). Dollar need not be the last character of the pattern if a number of alternatives are involved, but it should be the last item in any branch in which it appears. Dollar has no special meaning in a character class.

#### FULL STOP (PERIOD, DOT)

Outside a character class, a dot in the pattern matches any one character in the subject, including a non-printing character, but not (by default) newline. The handling of dot is entirely independent of the handling of circumflex and dollar, the only relationship being that they both involve newline characters. Dot has no special meaning in a character class.

#### SQUARE BRACKETS

An opening square bracket introduces a character class, terminated by a closing square bracket. A closing square bracket on its own is not special. If a closing square bracket is required as a member of the class, it should be the first data character in the class (after an initial circumflex, if present) or escaped with a backslash.

A character class matches a single character in the subject. A matched character must be in the set of characters defined by the class, unless the first character in the class definition is a circumflex, in which case the subject character must not be in the set defined by the class. If a circumflex is actually required as a member of the class, ensure it is not the first character, or escape it with a backslash.

For example, the character class [aeiou] matches any lower case vowel, while [^aeiou] matches any character that is not a lower case vowel. Note that a circumflex is just a convenient notation for specifying the characters which are in the class by enumerating those that are not. It is not an assertion: it still consumes a character from the subject string, and fails if the current pointer is at the end of the string.

When caseless matching is set, any letters in a class represent both their upper case and lower case versions, so for example, a caseless [aeiou] matches "A" as well as "a", and a caseless [^aeiou] does not match "A", whereas a caseful version would. PCRE does not support the concept of case for characters with values greater than 255. A class such as [^a] will always match a newline.

The minus (hyphen) character can be used to specify a range of characters in a character class. For example, [d-m] matches any letter between d and m, inclusive. If a minus character is required in a class, it must be escaped with a backslash or appear in a position where it cannot be interpreted as indicating a range, typically as the first or last character in the class.

It is not possible to have the literal character "]" as the end character of a range. A pattern such as [W-]46] is interpreted as a class of two characters ("W" and "-") followed by a literal string "46]", so it would match "W46]" or "-46]". However, if the "]" is escaped with a backslash it is interpreted as the end of range, so [W-\]46] is interpreted as a single class containing a range followed by two separate characters. The octal or hexadecimal representation of "]" can also be used to end a range.

The character types \d, \D, \s, \S, \w, and \W may also appear in a character class, and add the characters that they match to the class. For example, [\dABCDEF] matches any hexadecimal digit. A circumflex can conveniently be used with the upper case character types to specify a more restricted set of characters than the matching lower case type. For example, the class [^\W_] matches any letter or digit, but not underscore.

All non-alphameric characters other than \, -, ^ (at the start) and the terminating ] are non-special in character classes, but it does no harm if they are escaped.

#### VERTICAL BAR

Vertical bar characters are used to separate alternative patterns. For example, the pattern

gilbert|sullivan

matches either "gilbert" or "sullivan". Any number of alternatives may appear, and an empty alternative is permitted (matching the empty string). The matching process tries each alternative in turn, from left to right, and the first one that succeeds is used. If the alternatives are within a subpattern (defined below), "succeeds" means matching the rest of the main pattern as well as the alternative in the subpattern.

#### INTERNAL OPTION SETTING

The settings of the PCRE_CASELESS, PCRE_MULTILINE, PCRE_DOTALL, and PCRE_EXTENDED options can be changed from within the pattern by a sequence of Perl option letters enclosed between "(?" and ")". The option letters are

           i  for PCRE_CASELESS
           m  for PCRE_MULTILINE
           s  for PCRE_DOTALL
           x  for PCRE_EXTENDED

For example, (?im) sets caseless, multiline matching. It is also possible to unset these options by preceding the letter with a hyphen, and a combined setting and unsetting such as (?im-sx), which sets PCRE_CASELESS and PCRE_MULTILINE while unsetting PCRE_DOTALL and PCRE_EXTENDED, is also permitted. If a letter appears both before and after the hyphen, the option is unset.

When an option change occurs at top level (that is, not inside subpattern parentheses), the change applies to the remainder of the pattern that follows. If the change is placed right at the start of a pattern, PCRE extracts it into the global options (and it will therefore show up in data extracted by the pcre_fullinfo() function).

An option change within a subpattern affects only that part of the current pattern that follows it, so

(a(?i)b)c

matches abc and aBc and no other strings (assuming PCRE_CASELESS is not used). By this means, options can be made to have different settings in different parts of the pattern. Any changes made in one alternative do carry on into subsequent branches within the same subpattern. For example,

(a(?i)b|c)

matches "ab", "aB", "c", and "C", even though when matching "C" the first branch is abandoned before the option setting. This is because the effects of option settings happen at compile time. There would be some very weird behaviour otherwise.

The PCRE-specific options PCRE_UNGREEDY and PCRE_EXTRA can be changed in the same way as the Perl-compatible options by using the characters U and X respectively. The (?X) flag setting is special in that it must always occur earlier in the pattern than any of the additional features it turns on, even when it is at top level. It is best put at the start.

#### SUBPATTERNS

Subpatterns are delimited by parentheses (round brackets), which can be nested. Marking part of a pattern as a subpattern does two things:

1. It localizes a set of alternatives. For example, the pattern

cat(aract|erpillar|)

matches one of the words "cat", "cataract", or "caterpillar". Without the parentheses, it would match "cataract", "erpillar" or the empty string.

2. It sets up the subpattern as a capturing subpattern (as defined above). When the whole pattern matches, that portion of the subject string that matched the subpattern is passed back to the caller via the ovector argument of pcre_exec(). Opening parentheses are counted from left to right (starting from 1) to obtain the numbers of the capturing subpatterns.

For example, if the string "the red king" is matched against the pattern

the ((red|white) (king|queen))

the captured substrings are "red king", "red", and "king", and are numbered 1, 2, and 3, respectively.

The fact that plain parentheses fulfil two functions is not always helpful. There are often times when a grouping subpattern is required without a capturing requirement. If an opening parenthesis is followed by a question mark and a colon, the subpattern does not do any capturing, and is not counted when computing the number of any subsequent capturing subpatterns. For example, if the string "the white queen" is matched against the pattern

the ((?:red|white) (king|queen))

the captured substrings are "white queen" and "queen", and are numbered 1 and 2. The maximum number of capturing subpatterns is 65535, and the maximum depth of nesting of all subpatterns, both capturing and non-capturing, is 200.

As a convenient shorthand, if any option settings are required at the start of a non-capturing subpattern, the option letters may appear between the "?" and the ":". Thus the two patterns

           (?i:saturday|sunday)
           (?:(?i)saturday|sunday)

match exactly the same set of strings. Because alternative branches are tried from left to right, and options are not reset until the end of the subpattern is reached, an option setting in one branch does affect subsequent branches, so the above patterns match "SUNDAY" as well as "Saturday".

#### REPETITION

Repetition is specified by quantifiers, which can follow any of the following items:

           a literal data character
           the . meta-character
           the \C escape sequence
           escapes such as \d that match single characters
           a character class
           a back reference (see next section)
           a parenthesized subpattern (unless it is an assertion)

The general repetition quantifier specifies a minimum and maximum number of permitted matches, by giving the two numbers in curly brackets (braces), separated by a comma. The numbers must be less than 65536, and the first must be less than or equal to the second. For example:

z{2,4}

matches "zz", "zzz", or "zzzz". A closing brace on its own is not a special character. If the second number is omitted, but the comma is present, there is no upper limit; if the second number and the comma are both omitted, the quantifier specifies an exact number of required matches. Thus

[aeiou]{3,}

matches at least 3 successive vowels, but may match many more, while

\d{8}

matches exactly 8 digits. An opening curly bracket that appears in a position where a quantifier is not allowed, or one that does not match the syntax of a quantifier, is taken as a literal character. For example, {,6} is not a quantifier, but a literal string of four characters.

The quantifier {0} is permitted, causing the expression to behave as if the previous item and the quantifier were not present.

For convenience (and historical compatibility) the three most common quantifiers have single-character abbreviations:

           *    is equivalent to {0,}
           +    is equivalent to {1,}
           ?    is equivalent to {0,1}

It is possible to construct infinite loops by following a subpattern that can match no characters with a quantifier that has no upper limit, for example:

(a?)*

Earlier versions of Perl and PCRE used to give an error at compile time for such patterns. However, because there are cases where this can be useful, such patterns are now accepted, but if any repetition of the subpattern does in fact match no characters, the loop is forcibly broken.

By default, the quantifiers are "greedy", that is, they match as much as possible (up to the maximum number of permitted times), without causing the rest of the pattern to fail. The classic example of where this gives problems is in trying to match comments in C programs. These appear between the sequences /* and */ and within the sequence, individual * and / characters may appear. An attempt to match C comments by applying the pattern

/\*.*\*/

to the string

           /* first command */  not comment  /* second comment */

fails, because it matches the entire string owing to the greediness of the .* item.

However, if a quantifier is followed by a question mark, it ceases to be greedy, and instead matches the minimum number of times possible, so the pattern

/\*.*?\*/

does the right thing with the C comments. The meaning of the various quantifiers is not otherwise changed, just the preferred number of matches. Do not confuse this use of question mark with its use as a quantifier in its own right. Because it has two uses, it can sometimes appear doubled, as in

\d??\d

which matches one digit by preference, but can match two if that is the only way the rest of the pattern matches.

If the PCRE_UNGREEDY option is set (an option which is not available in Perl), the quantifiers are not greedy by default, but individual ones can be made greedy by following them with a question mark. In other words, it inverts the default behaviour.

When a parenthesized subpattern is quantified with a minimum repeat count that is greater than 1 or with a limited maximum, more store is required for the compiled pattern, in proportion to the size of the minimum or maximum. If a pattern starts with .* or .{0,} and the PCRE_DOTALL option (equivalent to Perl's /s) is set, thus allowing the . to match newlines, the pattern is implicitly anchored, because whatever follows will be tried against every character position in the subject string, so there is no point in retrying the overall match at any position after the first. PCRE normally treats such a pattern as though it were preceded by \A.

In cases where it is known that the subject string contains no newlines, it is worth setting PCRE_DOTALL in order to obtain this optimization, or alternatively using ^ to indicate anchoring explicitly.

However, there is one situation where the optimization cannot be used. When .* is inside capturing parentheses that are the subject of a backreference elsewhere in the pattern, a match at the start may fail, and a later one succeed. Consider, for example:

(.*)abc\1

If the subject is "xyz123abc123" the match point is the fourth character. For this reason, such a pattern is not implicitly anchored.

When a capturing subpattern is repeated, the value captured is the substring that matched the final iteration. For example, after

(tweedle[dume]{3}\s*)+

has matched "tweedledum tweedledee" the value of the captured substring is "tweedledee". However, if there are nested capturing subpatterns, the corresponding captured values may have been set in previous iterations. For example, after

           /(a|(b))+/

### PCRE PERFORMANCE

Certain items that may appear in regular expression patterns are more efficient than others. It is more efficient to use a character class like [aeiou] than a set of alternatives such as (a|e|i|o|u). In general, the simplest construction that provides the required behaviour is usually the most efficient. Jeffrey Friedl's book contains a lot of discussion about optimizing regular expressions for efficient performance.

When a pattern begins with .* not in parentheses, or in parentheses that are not the subject of a backreference, and the PCRE_DOTALL option is set, the pattern is implicitly anchored by PCRE, since it can match only at the start of a subject string. However, if PCRE_DOTALL is not set, PCRE cannot make this optimization, because the . meta-character does not then match a newline, and if the subject string contains newlines, the pattern may match from the character immediately following one of them instead of from the very start. For example, the pattern

.*second

matches the subject "first\nand second" (where \n stands for a newline character), with the match starting at the seventh character. In order to do this, PCRE has to retry the match starting after every newline in the subject.

If you are using such a pattern with subject strings that do not contain newlines, the best performance is obtained by setting PCRE_DOTALL, or starting the pattern with ^.* to indicate explicit anchoring. That saves PCRE from having to scan along the subject looking for a newline to restart at.

Beware of patterns that contain nested indefinite repeats. These can take a long time to run when applied to a string that does not match. Consider the pattern fragment

(a+)*

This can match "aaaa" in 33 different ways, and this number increases very rapidly as the string gets longer. (The * repeat can match 0, 1, 2, 3, or 4 times, and for each of those cases other than 0, the + repeats can match different numbers of times.) When the remainder of the pattern is such that the entire match is going to fail, PCRE has in principle to try every possible variation, and this can take an extremely long time. An optimization catches some of the more simple cases such as

(a+)*b

where a literal character follows. Before embarking on the standard matching procedure, PCRE checks that there is a "b" later in the subject string, and if there is not, it fails the match immediately. However, when there is no following literal this optimization cannot be used. You can see the difference by comparing the behaviour of

(a+)*\d

with the pattern above. The former gives a failure almost instantly when applied to a whole line of "a" characters, whereas the latter takes an appreciable time with strings longer than about 20 characters.

## References

None.

## Warnings

Regular expressions are case-sensitive. The pattern 'AAAA' will not match the sequence 'aaaa'. For this reason, both your pattern and the input sequences are converted to upper-case.

## Diagnostic Error Messages

None.

## Exit status

Always returns 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
fuzznuc | Search for patterns in nucleotide sequences
fuzztran | Search for patterns in protein sequences (translated)
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences

Other EMBOSS programs allow you to search for simple patterns and may be easier for the user who has never used regular expressions before:

- fuzznuc - Nucleic acid pattern search
- fuzzpro - Protein pattern search
- fuzztran - Protein pattern search after translation

## Author(s)

Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

Written (1999) - Peter Rice.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None