CSC

preg

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Function

Description

preg searches for matches of the supplied regular expression to the input protein sequence(s). A regular expression is a way of specifying an ambiguous pattern to search for. The output is a standard EMBOSS report file with details of any matches.

Usage

% preg 
Regular expression search of protein sequence(s)
Input protein sequence(s): tsw:*_rat
Regular expression pattern: IA[QWF]A
Output report [arf3_rat.preg]: 

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

Command line arguments

Regular expression search of protein sequence(s)
Version: EMBOSS:6.4.0.0

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

   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 and exit. 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
   -version            boolean    Report version number and exit

Input file format

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

Input files for usage example

Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.

By default, the report is in 'seqtable' format.

Output files for usage example

File: arf3_rat.preg

########################################
# Program: preg
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: preg
#    -sequence "tsw:*_rat"
#    -pattern "IA[QWF]A"
# Report_format: seqtable
# Report_file: arf3_rat.preg
########################################

#=======================================
#
# Sequence: ARF3_RAT     from: 1   to: 181
# HitCount: 0
#
# Pattern: IA[QWF]A
#
#=======================================

  Start     End Pattern Sequence

#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: UBR5_RAT     from: 1   to: 920
# HitCount: 1
#
# Pattern: IA[QWF]A
#
#=======================================

  Start     End Pattern         Sequence
    421     424 regex: IA[QWF]A IAQA

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

#---------------------------------------
# Total_sequences: 2
# Total_length: 1101
# Reported_sequences: 2
# Reported_hitcount: 1
#---------------------------------------

Data files

Notes

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. '^M' matches a methionine 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. 'R$' matches an arginine at the end of the sequence)

()

groups a pattern. This is commonly used with '|' (eg. '(ACD)|(VWY)' matches either the first 'ACD' or the second 'VWY' pattern )

|

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 these examples from the PROSITE patterns database:

'[STAGCN][RKH][LIVMAFY]$'

which is the 'Microbodies C-terminal targeting signal'.

'LP.TG[STGAVDE]'

which is the 'Gram-positive cocci surface proteins anchoring hexapeptide'.

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

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

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

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

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)

SQUARE BRACKETS

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

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

       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

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

       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

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

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

Comments