I've been enjoying the powerful function aregexec that allows me to mine strings in a fuzzy way.
For that I can search for a string of nucleotide "ATGGCTTCGTC" within a DNA section with defined allowance of insertion, deletion and substitute.
However, it only show me the first match without finishing the whole string. For example,
If I run
aregexec("a","adfasdfasdfaa")
only the first "a" will show up from the result. I'd like to see all the matches.
I wonder if there are other more powerful functions or a argument to be added to this one.
Thank you very much.
P.S. I explained the fuzzy search poorly. I mean, the match doesn't have to be perfect. Say if I allow an substitution of one character, and search AATTGG in ctagtactaAATGGGatctgct, the capital part will be considered a match. I can similarly allow insertions and deletions of certain characters.
gregexpr will show every time there is the pattern in the string, like in this example.
gregexpr("as","adfasdfasdfaa")
There are many more information if you use ?grep in R, it will explain every aspect of using regex.
Related
this is my first entry on stack overflow, so please be indulgent if my post might have some lack in terms of quality.
I want to learn some webscraping with R and started with a simple example --> Extracting a table from a Wikipedia site.
I managed to download the specific page and identified the HTML sections I am interested in:
<td style="text-align:right">511.000.000\n</td>
Now I want to extract the number in the data from the table by using regex. So i created a regex, which should match the structure of the number from my point of view:
pattern<-"\\d*\\.\\d*\\.\\d*\\.\\d*\\."
I also tried other variations but none of them found the number within the HTML code. I wanted to keep the pattern open as the numbers might be hundreds, thousand, millions, billions.
My questions: The number is within the HTML code, might it be
necessary to include some code for the non-number code (which should
not be extracted...)
What would be the correct version for the
pattern to identify the number correctly?
Thank you very much for your support!!
So many stars implies a lot of backtracking.
One point further, using \\d* would match more than 3 digits in any group and would also match a group with no digit.
Assuming your numbers are always integers, formatted using a . as thousand separator, you could use the following: \\d{1,3}(?:\\.\\d{3})* (note the usage of non-capturing group construct (?:...) - implying the use of perl = TRUE in arguments, as mentioned in Regular Expressions as used in R).
Look closely at your regex. You are assuming that the number will have 4 periods (\\.) in it, but in your own example there are only two periods. It's not going to match because while the asterisk marks \\d as optional (zero or more), the periods are not marked as optional. If you add a ? modifier after the 3rd and 4th period, you may find that your pattern starts matching.
I am attempting to use a fairly complex REGEX expression (see REGEX101 demos below), which I amended slightly from one created by an expert on this site. It parses specific patterns of log events:
1EXE_IN1EXE_CO2CONTENT_ACCESS3CONTENT_ACCESS
These log sequences will always begin with a random selection of EXE_IN or EXE_CO events, preceded sequence numbers. These selections can be any number, in any order. In this case, we just have two EXE events but this may be 200. Or 1. Note that there is a sequence number and we need to capture it.
The second part of the sequence will always be a series of digit-prefaced CONTENT.ACCESS events. Again from 1 to infinity in length.
The following demo shows a working example and probably conveys the concept better than I can : Demo 1
It nicely captures a full match, sequence number, and event in separate groups.
I need to add a timestamp to the pattern (after the sequence number, with a preceding underscore), and then parse this event log e.g.
1_11/08/2014 23:03EXE_IN1_11/08/2014 23:03EXE_CO2_12/08/2014 09:17CONTENT_ACCESS3_13/08/2014 09:17CONTENT_ACCESS
I need to capture the timestamps as well.
I attempted to adjust the regex expression, with mixed results. Please see this demo: demo2
Ideally I'd like to see something like this for each event:
Match n
Full match 266-308 `2_12/08/2014 09:17CONTENT_ACCESS`
Group 1. 266-267 `2`
Group 2. 268-284 `12/08/2014 09:17`
Group 3. 284-308 `CONTENT_ACCESS`
I hope you can help me. REGEX101 pcre testing is sufficient (for the record, I am using perl-compatible str_match_all_perl function in R).
Many thanks in advance.
(\d+)_(.*?)(EXE_CO|EXE_IN|CONTENT_ACCESS)
https://regex101.com/r/EHHcKm/1
Due to comments it was changed to (?:\G(?!^)(?(?=\d+_\d{2}\/\d{2}\/\d{4}\s\d{2}\:\d{2}(?:EXE_CO|EXE_IN))(?<!\d_\d{2}\/\d{2}\/\d{4}\s\d{2}\:\d{2}CONTENT_ACCESS))|(?=(?:\d+_\d{2}\/\d{2}\/\d{4}\s\d{2}\:\d{2}(?:EXE_CO|EXE_IN))+(?:\d+_\d{2}\/\d{2}\/\d{4}\s\d{2}\:\d{2}CONTENT_ACCESS)+))(\d+)_(\d{2}\/\d{2}\/\d{4}\s\d{2}\:\d{2})(EXE_CO|EXE_IN|CONTENT_ACCESS)
https://regex101.com/r/EHHcKm/3
Ans also another version, which is shorter
(?:\G(?!^)(?(?=\d+_.{16}(?:EXE_CO|EXE_IN))(?<!\d_.{16}CONTENT_ACCESS))|(?=(?:\d+_.{16}(?:EXE_CO|EXE_IN))+(?:\d+_.{16}CONTENT_ACCESS)+))(\d+)_(.{16})(EXE_CO|EXE_IN|CONTENT_ACCESS)
https://regex101.com/r/EHHcKm/4
And even more shorter (?:\G(?!^)(?(?=\d+_.{16}E)(?<!S))|(?=(?:\d+_.{16}(?:EXE_CO|EXE_IN))+\d+_.{16}C))(\d+)_(.{16})(EXE_CO|EXE_IN|CONTENT_ACCESS)
https://regex101.com/r/EHHcKm/5
And super short (?:\G|(?=\d+_.{16}E.*CON))(\d+)_(.*?)(EXE_CO|EXE_IN|CONTENT_ACCESS)
https://regex101.com/r/EHHcKm/8
I have a double challenge.
First, I want to match lines that contain two (or eventually more) specified words within certain distance in whatever order.
Using lookaround I manage to select lines matching two or more words, regardless of the order within they occur. I can also easily add more words to be found in the same line, so it this can also be applied without much effort when more word must occur in order to be selected. The disadvantage is that can't detail the maximal distance between them.
^(?=.*\john)(?=.*\jack).*$
By using the pipe operator I can detail both orders in which the terms may occur as well as the accepted distance between them, but when more words should be matched the code becomes lengthy and errorsensitive.
jack.{0,100}john|john.{0,100}jack
Is there a way to combine the respective advantages of both approaches in one regular expression?
Second, ideally I would like that only 'jack' and 'john' (and are selected in the line but not the whole line.
Is there a possibility to do this all at once?
For this case, you have to use the second approach. But it can't be possible with regex alone.. You have to ask for language tools help like paste in-order to build a regex (given in the second format).
In python, I would do like below to create a long regex.
>>> def create_reg(lis):
out = []
for i in lis:
out.append(''.join(i) + '|' + ''.join([i[2],i[1], i[0]]))
return '(?:' + '|'.join(out) + ')'
>>> lst = [('john', '{0,100}', 'jack'), ('foo', '{0,100}', 'bar')]
>>> create_reg(lst)
'(?:john{0,100}jack|jack{0,100}john|foo{0,100}bar|bar{0,100}foo)'
>>>
I'm attempting to clean up a database that, over the years, had acquired many duplicate records, with slightly different names. For example, in the companies table, there are names like "Some Company Limited" and "SOME COMPANY LTD!".
My plan was to export the offending tables into R, convert names to lower case, replace common synonyms (like "limited" -> "ltd"), strip out non-alphabetic characters and then use agrep to see what looks similar.
My first problem is that agrep only accepts a single pattern to match, and looping over every company name to match against the others is slow. (Some tables to be cleaned will have tens, possibly hundreds of thousands of names to check.)
I've very briefly looked at the tm package (JSS article), and it seems very powerful but geared towards analysing big chunks of text, rather than just names.
I have a few related questions:
Is the tm package appropriate for this sort of task?
Is there a faster alternative to agrep? (Said function uses the
Levenshtein edit distance which is anecdotally slow.)
Are there other suitable tools in R, apart from agrep and tm?
Should I even be doing this in R, or should this sort of thing be
done directly in the database? (It's an Access database, so I'd
rather avoid touching it if possible.)
If you're just doing small batches that are relatively well-formed, then the compare.linkage() or compare.dedup() functions in the RecordLinkage package should be a great starting point. But if you have big batches, then you might have to do some more tinkering.
I use the functions jarowinkler(), levenshteinSim(), and soundex() in RecordLinkage to write my own function that use my own weighting scheme (also, as it is, you can't use soundex() for big data sets with RecordLinkage).
If I have two lists of names that I want to match ("record link"), then I typically convert both to lower case and remove all punctuation. To take care of "Limited" versus "LTD" I typically create another vector of the first word from each list, which allows extra weighting on the first word. If I think that one list may contain acronyms (maybe ATT or IBM) then I'll acronym-ize the other list. For each list I end up with a data frame of strings that I would like to compare that I write as separate tables in a MySQL database.
So that I don't end up with too many candidates, I LEFT OUTER JOIN these two tables on something that has to match between the two lists (maybe that's the first three letters in each list or the first three letters and the first three letters in the acronym). Then I calculate match scores using the above functions.
You still have to do a lot of manual inspection, but you can sort on the score to quickly rule out non-matches.
Maybe google refine could help. It looks maybe more fitted if you have lots of exceptions and you don't know them all yet.
What you're doing is called record linkage, and it's been a huge field of research over many decades already. Luckily for you, there's a whole bunch of tools out there that are ready-made for this sort of thing. Basically, you can point them at your database, set up some cleaning and comparators (like Levenshtein or Jaro-Winkler or ...), and they'll go off and do the job for you.
These tools generally have features in place to solve the performance issues, so that even though Levenshtein is slow they can run fast because most record pairs never get compared at all.
The Wikipedia link above has links to a number of record linkage tools you can use. I've personally written one called Duke in Java, which I've used successfully for exactly this. If you want something big and expensive you can buy a Master Data Management tool.
In your case probably something like edit-distance calculation would work, but if you need to find near duplicates in larger text based documents, you can try
http://www.softcorporation.com/products/neardup/
I'd like to find patterns and sort them by number of occurrences on an HEX file I have.
I am not looking for some specific pattern, just to make some statistics of the occurrences happening there and sort them.
DB0DDAEEDAF7DAF5DB1FDB1DDB20DB1BDAFCDAFBDB1FDB18DB23DB06DB21DB15DB25DB1DDB2EDB36DB43DB59DB32DB28DB2ADB46DB6FDB32DB44DB40DB50DB87DBB0DBA1DBABDBA0DB9ADBA6DBACDBA0DB96DB95DBB7DBCFDBCBDBD6DB9CDBB5DB9DDB9FDBA3DB88DB89DB93DBA5DB9CDBC1DBC1DBC6DBC3DBC9DBB3DBB8DBB6DBC8DBA8DBB6DBA2DB98DBA9DBB9DBDBDBD5DBD9DBC3DB9BDBA2DB84DB83DB7DDB6BDB58DB4EDB42DB16DB0DDB01DB02DAFCDAE9DAE5DAD9DAE2DAB7DA9BDAA6DA9EDAAADAC9DACADAC4DA92DA90DA84DA89DA93DAA9DA8CDA7FDA62DA53DA6EDA
That's an excerpt of the HEX file, and as an example I'd like to get:
XX occurrences of BDBDBD
XX occurrences of B93D
Is there a way to mine the file to generate that output?
Sure. Use a sliding window to create the counts (The link is for Perl, but it seems general enough to understand the algorithm). Your patterns are named N-grams. You will have to limit the maximal pattern, though.
This is a pretty classic CS problem. The code in general is non-trivial to implement as it will require at least one full parse of the sequence, and depending on your efficiency and memory/processor constraints might require several. See here.
You will need to partition your input string in some way to ensure that you get a good subsequence across it.
If there is a specific problem we might be able to help more, but the general strategy is in the Wikipedia article above.
You can use Regular Expressions to make a pattern to search for.
The regex needed would be very simple. Just use the exact phrase you're searching for. Then there should be a regular expression function in the language you're using (you didn't specify) that can count the number of matches.
Use that to create a simple counter.