I am writing a script in Perl which searches for a motif(substring) in protein sequence(string). The motif sequence to be searched (or substring) is hhhDDDssEExD, where:
h is any hydrophobic amino acid
s is any small amino acid
x is any amino acid
h,s,x can have more than one value separately
Can more than one value be assigned to one variable? If yes, how should I do that? I want to assign a list of multiple values to a variable.
It seems like you want some kind of pattern matching. This can be done with strings using regular expressions.
You can use character classes in your regular expression. The classes you mentioned would be:
h -> [VLIM]
s -> [AG]
x -> [A-IK-NP-TV-Z]
The last one means "A to I, K to N, P to T, V to Z".
The regular expression for your example would be:
/[VLIM]{3}D{3}[AG]{2}E{2}[A-IK-NP-TV-Z]D/
I am no great expert in perl, so there is quite possibly a quicker way to this, but it seems like the match operator "//" in list context is what you need. When you assign the result of a match operation to a list, the match operator takes on list context and returns a list with each of the parenthesis delimited sub-expressions. If you specify global matches with the "g" flag, it will return a list of all the matches of each sub-expression. Example:
# print a list of each match for "x" in "xxx"
#aList = ("xxx" =~ /(x)/g);
print(join(".", #aList));
Will print out
x.x.x
I'm assuming you have a regular expression for each of those 5 types h, D, s, E, and x. You didn't say whether each of these parts is a single character or multiple, so I'm going to assume they can be multiple characters. If so, your solution might be something like this:
$h = ""; # Insert regex to match "h"
$D = ""; # Insert regex to match "D"
$s = ""; # Insert regex to match "s"
$E = ""; # Insert regex to match "E"
$x = ""; # Insert regex to match "x"
$sequenceRE = "($h){3}($D){3}($s){2}($E){2}($x)($D)"
if ($line =~ /$sequenceRE/) {
$hPart = $1;
$sPart = $3;
$xPart = $5;
#hValues = ($hPart =~ /($h)/g);
#sValues = ($sPart =~ /($s)/g);
#xValues = ($xPart =~ /($x)/g);
}
I'm sure there is something I've missed, and there are some subtleties of perl that I have overlooked, but this should get you most of the way there. For more information, read up on perl's match operator, and regular expressions.
I could be way off, but it sounds like you want an object with a built in method to output as a string.
If you start with a string, like the one you mentioned, you could pass the string to the class as a new object, use regular expressions like everyone has already suggested to parse out the chunks that you would then assign as variables to that object. Finally, you could have it output a string based on the variables of that object, for instance:
$string = "COHOCOHOCOHOCOHOCOHOC";
$sugar = new Organic($string);
Class Organic {
$chem;
function __construct($chem) {
$hydro_find = "OHO";
$carb_find = "C";
$this-> hydro = preg_find ($hydro_find, $chem);
$this -> carb = preg_find ($carb_find, $chem);
function __TO_STRING() {
return $this->carb."="$this->hydro;
}
}
echo $sugar;
Okay, that kind of fell apart in the end, and it was pseudo-php, not perl. But if I understand your question correctly, you are looking for a way to get all of the info from the string but keep it tied to that string. That would be objects and classes.
You probably want an array (or arrayref) or a pattern (qr//).
Or maybe Quantum::Superpositions.
Related
I use string.format(str, regex) of LUA to fetch some key word.
local RICH_TAGS = {
"texture",
"img",
}
--\[((img)|(texture))=
local START_OF_PATTER = "\\[("
for index = 1, #RICH_TAGS - 1 do
START_OF_PATTER = START_OF_PATTER .. "(" .. RICH_TAGS[index]..")|"
end
START_OF_PATTER = START_OF_PATTER .. "("..RICH_TAGS[#RICH_TAGS].."))"
function RichTextDecoder.decodeRich(str)
local result = {}
print(str, START_OF_PATTER)
dump({string.find(str, START_OF_PATTER)})
end
output
hello[img=123] \[((texture)|(img))
dump from: [string "utils/RichTextDecoder.lua"]:21: in function 'decodeRich'
"<var>" = {
}
The output means:
str = hello[img=123]
START_OF_PATTER = \[((texture)|(img))
This regex works well with some online regex tools. But it find nothing in LUA.
Is there any wrong using in my code?
You cannot use regular expressions in Lua. Use Lua's string patterns to match strings.
See How to write this regular expression in Lua?
Try dump({str:find("\\%[%("))})
Also note that this loop:
for index = 1, #RICH_TAGS - 1 do
START_OF_PATTER = START_OF_PATTER .. "(" .. RICH_TAGS[index]..")|"
end
will leave out the last element of RICH_TAGS, I assume that was not your intention.
Edit:
But what I want is to fetch several specific word. For example, the
pattern can fetch "[img=" "[texture=" "[font=" any one of them. With
the regex string I wrote in my question, regex can do the work. But
with Lua, the way to do the job is write code like string.find(str,
"[img=") and string.find(str, "[texture=") and string.find(str,
"[font="). I wonder there should be a way to do the job with a single
pattern string. I tryed pattern string like "%[%a*=", but obviously it
will fetch a lot more string I need.
You cannot match several specific words with a single pattern unless they are in that string in a specific order. The only thing you could do is to put all the characters that make up those words into a class, but then you risk to find any word you can build from those letters.
Usually you would match each word with a separate pattern or you match any word and check if the match is one of your words using a look up table for example.
So basically you do what a regex library would do in a few lines of Lua.
I have a list of records that are character vectors. Here's an example:
'1mil_0,1_1_1_lb200_ks_drivers_sorted.csv'
'1mil_0_1_lb100_ks_drivers_sorted.csv'
'1mil_1_1_lb2_100_100_ks_drivers_sorted.csv'
'1mil_1_1_lb100_ks_drivers_sorted.csv'
From these names I would like to extract whatever's between the two substrings 1mil_ and _ks_drivers_sorted.csv.
So in this case the output would be:
0,1_1_1_lb200
0_1_lb100
1_1_lb2_100_100
1_1_lb100
I'm using MATLAB so I thought to use regexp to do this, but I can't understand what kind of regular expression would be correct.
Or are there some other ways to do this without using regexp?
Let the data be:
x = {'1mil_0,1_1_1_lb200_ks_drivers_sorted.csv'
'1mil_0_1_lb100_ks_drivers_sorted.csv'
'1mil_1_1_lb2_100_100_ks_drivers_sorted.csv'
'1mil_1_1_lb100_ks_drivers_sorted.csv'};
You can use lookbehind and lookahead to find the two limiting substrings, and match everything in between:
result = cellfun(#(c) regexp(c, '(?<=1mil_).*(?=_ks_drivers_sorted\.csv)', 'match'), x);
Or, since the regular expression only produces one match, the following simpler alternative can be used (thanks #excaza for noticing):
result = regexp(x, '(?<=1mil_).*(?=_ks_drivers_sorted\.csv)', 'match', 'once');
In your example, either of the above gives
result =
4×1 cell array
'0,1_1_1_lb200'
'0_1_lb100'
'1_1_lb2_100_100'
'1_1_lb100'
For me the easy way to do this is just use espace or nothing to replace what you don't need in your string, and the rest is what you need.
If is a list, you can use a loop to do this.
Exemple to replace "1mil_" with "" and "_ks_drivers_sorted.csv" with ""
newChr = strrep(chr,'1mil_','')
newChr = strrep(chr,'_ks_drivers_sorted.csv','')
I have a big hash with a lot of elements.
%my_hash = ();
# filling of %my_hash automaticly
$my_variable;
# set the value of $my_variable within a loop
Now I want to find the value of $my_variablewithin %my_hash. I tried it with
if(grep {/$my_variable/} keys %my_hash){
$my_new_variable = #here should be the element of %my_hash which makes the statement true
}
how to do that?
Edit: The problem is not the whole $my_variable will be find at %my_hash, e.g.
$my_variable = astring
$modules_by_path{"this_is_a_longer_astring"} = (something)
now I want to find this...
If you're looking only for one particular key from %my_hash,
if (my ($my_new_variable) = grep /\Q$my_variable/, keys %my_hash) {
..
}
or
if (my #keys = grep /\Q$my_variable/, keys %my_hash) { .. }
if there are more keys which match specified regex. (use \Q prefix if $my_variable is not regex but literal string to be matched).
You can use grep, but you need to put it in scalar context to get the result you want. You also need to escape the contents of $my_variable if there's any chance that it contains any regex metacharacters.
This uses \Q to escape the non-alphanumeric characters, and leaves all the hash keys that match in #matching_keys. It's up to you to decide what to do if there's more than one match!
my #matching_keys = grep /\Q$my_variable/, keys %my_hash;
I suspect that there's a better way to do this. It's spoiling the whole point of hashes to search through them like that, and I think a better data design would help. But I can't say any more unless you describe your data and your application.
if you want to match every key of your hash, you have to iterate through them in a loop as well. this is how i would do it, don't know if it is the most elegant way though:
#!/usr/bin/env perl
use strict;
use warnings;
my %hash = (
foo => 1,
bar => 1,
baz => 1,
);
my $variable = "bar";
my $new_variable;
for my $key (keys %hash){
if ($key =~ /$variable/){
$new_variable = $hash{$key};
}
}
print $new_variable, "\n";
also, always try to write stuff like that with use strict; it will spare you of many classic mistakes.
I have string like
a;b;"aaa;;;bccc";deef
I want to split string based on delimiter ; only if ; is not inside double quotes. So after the split, it will be
a
b
"aaa;;;bccc"
deef
I tried using look-behind, but I'm not able to find a correct regular expression for splitting.
Regular expressions are probably not the right tool for this. If possible you should use a CSV library, specify ; as the delimiter and " as the quote character, this should give you the exact fields you are looking for.
That being said here is one approach that works by ensuring that there are an even number of quotation marks between the ; we are considering the split at and the end of the string.
;(?=(([^"]*"){2})*[^"]*$)
Example: http://www.rubular.com/r/RyLQyR8F19
This will break down if you can have escaped quotation marks within a string, for example a;"foo\"bar";c.
Here is a much cleaner example using Python's csv module:
import csv, StringIO
reader = csv.reader(StringIO.StringIO('a;b;"aaa;;;bccc";deef'),
delimiter=';', quotechar='"')
for row in reader:
print '\n'.join(row)
Regular expression will only get messier and break on even minor changes. You are better off using a csv parser with any scripting language. Perl built in module (so you don't need to download from CPAN if there are any restrictions) called Text::ParseWords allows you to specify the delimiter so that you are not limited to ,. Here is a sample snippet:
#!/usr/local/bin/perl
use strict;
use warnings;
use Text::ParseWords;
my $string = 'a;b;"aaa;;;bccc";deef';
my #ary = parse_line(q{;}, 0, $string);
print "$_\n" for #ary;
Output
a
b
aaa;;;bccc
deef
This is kind of ugly, but if you don't have \" inside your quoted strings (meaning you don't have strings that look like this ("foo bar \"badoo\" goo") you can split on the " first and then assume that all your even numbered array elements are, in fact, strings (and split the odd numbered elements into their component parts on the ; token).
If you *do have \" in your strings, then you'll want to first convert those into some other temporary token that you'll convert back later after you've performed your operation.
Here's a fiddle...
http://jsfiddle.net/VW9an/
var str = 'abc;def;ghi"some other dogs say \\"bow; wow; wow\\". yes they do!"and another; and a fifth'
var strCp = str.replace(/\\"/g,"--##--");
var parts = strCp.split(/"/);
var allPieces = new Array();
for(var i in parts){
if(i % 2 == 0){
var innerParts = parts[i].split(/\;/)
for(var j in innerParts)
allPieces.push(innerParts[j])
}
else{
allPieces.push('"' + parts[i] +'"')
}
}
for(var a in allPieces){
allPieces[a] = allPieces[a].replace(/--##--/g,'\\"');
}
console.log(allPieces)
Match All instead of Splitting
Answering long after the battle because no one used the way that seems the simplest to me.
Once you understand that Match All and Split are Two Sides of the Same Coin, you can use this simple regex:
"[^"]*"|[^";]+
See the matches in the Regex Demo.
The left side of the alternation | matches full quoted strings
The right side matches any chars that are neither ; nor "
I am reading from file. Based on value in one column, I want to assign my own class/tag to it.
These regexps:
'LTR*','MLT*','MST*' ...
belong to the class HERV.
'Charlie*','Looper*' ...
belong to the class DNA
Right now I have two arrays, one with regexps and one with respective classes:
my #array = map { qr{$_} } ('Alu*', 'HERV*', 'Charlie*' ...
my #classes = ('Alu', 'HERV', 'DNA', 'LINE' ...
So that I know that if my line matches Charlie*, it belongs to the class DNA.
To sum it up, for every line of the file I am looping the whole array and looking for match:
for my $i (0 .. $#array) {
if ($type =~ m/$array[$i]/) {
my $class=$classes[$i];
}
}
Of course, this is not too clever. It would be much better to say: "this group of regexps belongs to this class" which suggests use of hash.
However, I consider it quite inconvenient to loop all lines, than all keys of hashmap and then all values of certain keys and, when there is a match, use the key as the resulting class/tag. Is this good solution or not?
Thank you very much.
You can do something like this:
my %re = (
HERV=>qr/LTR|MLT|MST/,
DNA=> qr/Charlie|Looper/
);
my $class;
for (keys %re) {
$class = $_, last if ($type =~ $re{$_});
}
This will save you some regex compilation and one loop.
The CPAN module Text::Prefix::XS appears to do what you want: determine which if any of a list of prefixes match a given text. I have not used the module, but from what I can tell you would do something like:
my %prefix2class = ( LTR => 'HERV',
MLV => 'HERV',
...
Charlie => 'DNA' );
my $search = prefix_search_create( keys %prefix2class );
# ... now, for a given $type, no need to loop ...
my $pfx = prefix_search($search, $type);
my $class = $prefix2class{$pfx};
(Note: Your regexes look to me like shell-style/fnmatch-style patterns dubiously compiled as regexes, and from this I infer that you actually want simple prefix matching. Otherwise, the regex /Charlie*/, for example, would match Charli, Charlieeee, fooCharliebar, and so on — that seems unlikely to be representative of your "value in one column".)