i'm trying to find pattern search with specific constraints :
input pattern to be searched will be entered from std. input
R,W and Y will be anywhere in the pattern which should be replaced with below values before searching and so every combination possible for the pattern are to be searched in a sequence.
R = C or G
W = A or T
Y = A or G
[e.g, pattern may be AWTYCR and sequence may be ATCGATGAT....]
we have to find starting positions
Also one mismatch is allowed.
i.e., one character of the pattern may or maynot match while matching with the sequence.
output:
should be written into a file in a table format:
for example,
finding ATCR (R = C or G as above mentioned) in sequence ATCGAT will result in
S.no position the_matched_pattern
1 1 ATCG
2 1 ATCC
the match and mismatch may come in any position (i.e, in same position or in different position)
The following simple code is a starting point. It can be easily generalized to read the patterns from the file, read the sequence from the Fasta file; unique the results, etc.
sub trans_pat {
my $pat=shift;
$pat=~s/R/\[CG\]/g;
$pat=~s/W/\[AT\]/g;
$pat=~s/Y/\[AG\]/g;
return $pat;
}
sub find_pat {
my ($pat,$seq) = (#_);
print "Looking for pattern $pat\n";
while ($seq=~m/$pat/g) {
print "... match at $-[0]: $&\n";
};
}
my $read_pat="ATCR";
my $seq="ATCGATATCGAT";
# Looking for a perfect match
find_pat (trans_pat($read_pat),$seq);
# Allowing for a single mismatch
foreach $i (1..length $read_pat) {
my $mis_pat = $read_pat;
substr($mis_pat,$i-1,1) = ".";
find_pat (trans_pat($mis_pat),$seq);
}
A sample implementation:
perl -e 'sub trans {$pat=shift;$pat=~s/R/\[CG\]/g;return $pat};$read_pat="ATCR";$seq="ATCGATATCGAT";$pat=trans($read_pat);print "Looking for pattern $pat\n";while ($seq=~m/$pat/g) {print "... match at $-[0]: $&\n"};foreach $i (1..length $read_pat) {$mis_pat = $read_pat;substr($mis_pat,$i-1,1)=".";$pat=trans($mis_pat);print "Looking for pattern $pat\n"; while ($seq=~m/$pat/g) {print "... match at $-[0]: $&\n"}}'
Yields
Looking for pattern ATC[CG]
... match at 0: ATCG
... match at 6: ATCG
Looking for pattern .TC[CG]
... match at 0: ATCG
... match at 6: ATCG
Looking for pattern A.C[CG]
... match at 0: ATCG
... match at 6: ATCG
Looking for pattern AT.[CG]
... match at 0: ATCG
... match at 6: ATCG
Looking for pattern ATC.
... match at 0: ATCG
... match at 6: ATCG
Related
I need to write a regex which allows a group of 2 chars only once. This is my current regex :
^([A-Z]{2},)*([A-Z]{2}){1}$
This allows me to validate something like this :
AL,RA,IS,GD
AL
AL,RA
The problem is that it validates also AL,AL and AL,RA,AL.
EDIT
Here there are more details.
What is allowed:
AL,RA,GD
AL
AL,RA
AL,IS,GD
What it shouldn't be allowed:
AL,RA,AL
AL,AL
AL,RA,RA
AL,IS,AL
IS,IS,AL
IS,GD,GD
IS,GD,IS
I need that every group of two characters appears only once in the sequence.
Try something like this expression:
/^(?:,?(\b\w{2}\b)(?!.*\1))+$/gm
I have no knowledge of swift, so take it with a grain of salt. The idea is basically to only match a whole line while making sure that no single matched group occurs at a later point in the line.
First of all, let's shorten your pattern. It can be easily achieved since the length of each comma-separated item is fixed and the list items are only made up of uppercase ASCII letters. So, your pattern can be written as ^(?:[A-Z]{2}(?:,\b)?)+$. See this regex demo.
Now, you need to add a negative lookahead that will check the string for any repeating two-letter sequence at any distance from the start of string, and within any distance between each. Use
^(?!.*\b([A-Z]{2})\b.*\b\1\b)(?:[A-Z]{2}(?:,\b)?)+$
See the regex demo
Possible implementation in Swift:
func isValidInput(Input:String) -> Bool {
return Input.range(of: #"^(?!.*\b([A-Z]{2})\b.*\b\1\b)(?:[A-Z]{2}(?:,\b)?)+$"#, options: .regularExpression) != nil
}
print(isValidInput(Input:"AL,RA,GD")) // true
print(isValidInput(Input:"AL,RA,AL")) // false
Details
^ - start of string
(?!.*\b([A-Z]{2})\b.*\b\1\b) - a negative lookahead that fails the match if, immediately to the right of the current location, there is:
.* - any 0+ chars other than line break chars, as many as possible
\b([A-Z]{2})\b - a two-letter word as a whole word
.* - any 0+ chars other than line break chars, as many as possible
\b\1\b - the same whole word as in Group 1. NOTE: The word boundaries here are not necessary in the current scenario where the word length is fixed, it is two, but if you do not know the word length, and you have [A-Z]+, you will need the word boundaries, or other boundaries depending on the situation
(?:[A-Z]{2}(?:,\b)?)+ - 1 or more sequences of:
[A-Z]{2} - two uppercase ASCII letters
(?:,\b)? - an optional sequence: , only if followed with a word char: letter, digit or _. This guarantees that , won't be allowed at the end of the string
$ - end of string.
You can use a negative lookahead with a back-reference:
^(?!.*([A-Z]{2}).*\1).*
if, as in the all the examples in the question, it is known that the string contains only comma-separated pairs of capital letters. I will relax that assumption later in my answer.
Demo
The regex performs the following operations:
^ # match beginning of line
(?! # begin negative lookahead
.* # match 0+ characters (1+ OK)
([A-Z]{2}) # match 2 uppercase letters in capture group 1
.* # match 0+ characters (1+ OK)
\1 # match the contents of capture group 1
) # end negative lookahead
.* # match 0+ characters (the entire string)
Suppose now that one or more capital letters may appear between each pair of commas, or before the first comma or after the last comma, but it is only strings of two letters that cannot be repeated. Moreover, I assume the regex must confirm the regex has the desired form. Then the following regex could be used:
^(?=[A-Z]+(?:,[A-Z]+)*$)(?!.*(?:^|,)([A-Z]{2}),(?:.*,)?\1(?:,|$)).*
Demo
The regex performs the following operations:
^ # match beginning of line
(?= # begin pos lookahead
[A-Z]+ # match 1+ uc letters
(?:,[A-Z]+) # match ',' then by 1+ uc letters in a non-cap grp
* # execute the non-cap grp 0+ times
$ # match the end of the line
) # end pos lookahead
(?! # begin neg lookahead
.* # match 0+ chars
(?:^|,) # match beginning of line or ','
([A-Z]{2}) # match 2 uc letters in cap grp 1
, # match ','
(?:.*,) # match 0+ chars, then ',' in non-cap group
? # optionally match non-cap grp
\1 # match the contents of cap grp 1
(?:,|$) # match ',' or end of line
) # end neg lookahead
.* # match 0+ chars (entire string)
If there is no need check that the string contains only comma-separated strings of one or more upper case letters the postive lookahead at the beginning can be removed.
The text file abc.txt is an arbitrary article that has been scraped from the web. For example, it is as follows:
His name is "Donald" and he likes burger. On December 11, he married.
I want to extract only words in lower case and numbers except for all kinds of periods and quotes in the above article. In the case of the above example:
{his, name, is, Donald, and, he, likes, burger, on, December, 11, he, married}
My code is as follows:
filename = 'abc.txt';
fileID = fopen(filename,'r');
C = textscan(fileID,'%s','delimiter',{',','.',':',';','"','''});
fclose(fileID);
Cstr = C{:};
Cstr = Cstr(~cellfun('isempty',Cstr));
Is there any simple code to extract only alphabet words and numbers except all symbols?
Two steps are necessary as you want to convert certain words to lowercase.
regexprep converts words, which are either at the start of the string or follow a full stop and whitespace, to lower case.
In the regexprep function, we use the following pattern:
(?<=^|\. )([A-Z])
to indicate that:
(?<=^|\. ) We want to assert that before the word of interest either the start of string (^), or (|) a full stop (.) followed by whitespace are found. This type of construct is called a lookbehind.
([A-Z]) This part of the expression matches and captures (stores the match) a upper case letter (A-Z).
The ${lower($0)} component in the regex is called a dynamic expression, and replaces the contents of the captured group (([A-Z])) to lower case. This syntax is specific to the MATLAB language.
You can check the behaviour of the above expression here.
Once the lower case conversions have occurred, regexp finds all occurrences of one or more digits, lower case and upper case letters.
The pattern [a-zA-Z0-9]+ matches lower case letters, upper case letters and digits.
You can check the behavior of this regex here.
text = fileread('abc.txt')
data = {regexp(regexprep(text,'(?<=^|\. )([A-Z])','${lower($0)}'),'[a-zA-Z0-9]+','match')'}
>>data{1}
13×1 cell array
{'his' }
{'name' }
{'is' }
{'Donald' }
{'and' }
{'he' }
{'likes' }
{'burger' }
{'on' }
{'December'}
{'11' }
{'he' }
{'married' }
Write a program that accepts a sentence as console input and calculate the number of upper case letters , lower case letters and other characters.
Suppose the following input is supplied to the program:
Hello World;!#
Since this question sounds like a programming assignment, I've written this is a more-wordy manner. This is standard Python 3, not Jes.
#! /usr/bin/env python3
import sys
upper_case_chars = 0
lower_case_chars = 0
total_chars = 0
found_eof = False
# Read character after character from stdin, processing it in turn
# Stop if an error is encountered, or End-Of-File happens.
while (not found_eof):
try:
letter = str(sys.stdin.read(1))
except:
# handle any I/O error somewhat cleanly
break
if (letter != ''):
total_chars += 1
if (letter >= 'A' and letter <= 'Z'):
upper_case_chars += 1
elif (letter >= 'a' and letter <= 'z'):
lower_case_chars += 1
else:
found_eof = True
# write the results to the console
print("Upper-case Letters: %3u" % (upper_case_chars))
print("Lower-case Letters: %3u" % (lower_case_chars))
print("Other Letters: %3u" % (total_chars - (upper_case_chars + lower_case_chars)))
Note that you should modify the code to handle end-of-line characters yourself. Currently they're counted as "other". I've also left out handling of binary input, probably the str() will fail.
I've got a related thread in the site(My lex pattern doesn't work to match my input file, how to correct it?)
The problems I met, is about how "greedy" lex will do pattern match, e.g. I've got my lex file:
$ cat b.l
%{
#include<stdio.h>
%}
%%
"12" {printf("head\n");}
"34" {printf("tail\n");}
.* {printf("content\n");}
%%
What I wish to say is, when meet "12", print "head"; when meet "34", print "tail", otherwise print "content" for the longest match that doesn't contain either "12" or "34".
But the fact was, ".*" was a greedy match that whatever I input, it prints "content".
My requirement is, when I use
12sdf2dfsd3sd34
as input, the output should be
head
content
tail
So seems there're 2 possible ways:
1, To specify a match priority for ".*", it should work only when neither "12" and "34" works to match. Does lex support "priority"?
2, to change the 3rd expression, as to match any contiguous string that doesn't contain sub-string of "12", or "34". But how to write this regular expression?
Does (f)lex support priority?
(F)lex always produces the longest possible match. If more than one rule matches the same longest match, the first one is chosen, so in that case it supports priority. But it does not support priority for shorter matches, nor does it implement non-greedy matching.
How to match a string which does not contain one or more sequences?
You can, with some work, create a regular expression which matches a string not containing specified substrings, but it is not particularly easy and (f)lex does not provide a simple syntax for such regular expressions.
A simpler (but slightly less efficient) solution is to match the string in pieces. As a rough outline, you could do the following:
"12" { return HEAD; }
"34" { if (yyleng > 2) {
yyless(yyleng - 2);
return CONTENT;
}
else
return TAIL;
}
.|\n { yymore(); }
This could be made more efficient by matching multiple characters when there is not chance of skipping a delimiter; change the last rule to:
.|[^13]+ { yymore(); }
yymore() causes the current token to be retained, so that the next match appends to the current token rather than starting a new token. yyless(x) returns all but the first x characters to the input stream; in this case, that is used to cause the end delimiter 34 to be rescanned after the CONTENT token is identified.
(That assumes you actually want to tokenize the input stream, rather than just print a debugging message, which is why I called it an outline solution.)
diary_file = tempname();
diary(diary_file);
myFun();
diary('off');
output = fileread(diary_file);
I would like to search a string from output, but also to ignore spaces and upper/lower cases. Here is an example for what's in output:
the test : passed
number : 4
found = 'thetest:passed'
a = strfind(output,found )
How could I ignore spaces and cases from output?
Assuming you are not too worried about accidentally matching something like: 'thetEst:passed' here is what you can do:
Remove all spaces and only compare lower case
found = 'With spaces'
found = lower(found(found ~= ' '))
This will return
found =
withspaces
Of course you would also need to do this with each line of output.
Another way:
regexpi(output(~isspace(output)), found, 'match')
if output is a single string, or
regexpi(regexprep(output,'\s',''), found, 'match')
for the more general case (either class(output) == 'cell' or 'char').
Advantages:
Fast.
robust (ALL whitespace (not just spaces) is removed)
more flexible (you can return starting/ending indices of the match, tokenize, etc.)
will return original case of the match in output
Disadvantages:
more typing
less obvious (more documentation required)
will return original case of the match in output (yes, there's two sides to that coin)
That last point in both lists is easily forced to lower or uppercase using lower() or upper(), but if you want same-case, it's a bit more involved:
C = regexpi(output(~isspace(output)), found, 'match');
if ~isempty(C)
C = found; end
for single string, or
C = regexpi(regexprep(output, '\s', ''), found, 'match')
C(~cellfun('isempty', C)) = {found}
for the more general case.
You can use lower to convert everything to lowercase to solve your case problem. However ignoring whitespace like you want is a little trickier. It looks like you want to keep some spaces but not all, in which case you should split the string by whitespace and compare substrings piecemeal.
I'd advertise using regex, e.g. like this:
a = regexpi(output, 'the\s*test\s*:\s*passed');
If you don't care about the position where the match occurs but only if there's a match at all, removing all whitespaces would be a brute force, and somewhat nasty, possibility:
a = strfind(strrrep(output, ' ',''), found);