I am trying to use seqkit rmdup to remove duplicated sequences from my protein fasta files. However, it's only the accession numbers which are duplicated and not the description or sequences. See example below.
Host_331002_c0_seq1 95 1381 2 +
Host_331002_c0_seq1 1873 2112 1 +
So basically I want to set a flag which will stop at the first tab when searching the identifiers (stop after Host_331002_c0_seq1) otherwise I won't get any duplicates in my output file. This flag would fix it but I am not sure how to manipulate regex.
--id-regexp string regular expression for parsing ID (default "^(\\S+)\\s?")
Could you assist with this issue?
I just started learning all the programming languages and I am not certain how to change that.
Regex to match any zero or more characters up to the first tab excluding tab is
^[^\t]*
See proof.
Related
I use a translator tool to translate English into Simplified Chinese.
Now there is an issue with the period.
In English at the finish point of a sentence, we use full stop "."
In Simplified Chinese, it is "。"which looks like a small circle.
The translation tool mistakenly add this "small circle" / full stop to every major subtitles.
Is there a way to use Regex or other methods to scan the translated content, and replace any "small circle" / Chinese full stop symbol when the line has only 20 characters or less?
Some test data like below
<h1>这是一个测试。<h1>
这是一个测试，这是一个测试而已，希望去掉不需要的。
测试。
这是一个测试，这是一个测试而已，希望去掉不需要的第二行。
It shall turn into:
<h1>这是一个测试<h1>
这是一个测试，这是一个测试而已，希望去掉不需要的。
测试
这是一个测试，这是一个测试而已，希望去掉不需要的第二行。
Difference:
Line 1 it only has 10 characters, and shall have Chinese full stop removed.
Line 4 is a sub heading, it only has 4 characters, and shall have full stop removed too.
By the way, I was told 1 Chinese word is two English characters.
Is this possible?
I'm using the approach 2
Second: maybe this one is more accurate: if there is no comma in this line, it should not have a full stop.
to determine whether a full stop 。 should be removed.
Regex
/^(?=.*。)(?!.*，)([^。]*)。/mg
^ start of a line
(?=.*。) match a line that contains 。
(?!.*，) match a line that doesn't contain ，
([^。]*)。 anything that not a full stop before a full stop, put it in group 1
Substitution
$1
Check the test cases here
But do mind this only removes the first full stop.
If you want to remove all the full stops, you can try (?:\G|^)(?=.*。)(?!.*，)(.*?)。 but this only works for regex engines supports \G such as pcre.
Also, if you want to combine the two approaches(a line has no period ， and the length is less than 20 characters), you can try ^(?=.{1,20}$)(?=.*。)(?!.*，)([^。]*)。
I need to parse a large amount of data in a log file, ideally I can do this by splitting the file into a list where each entry in the list is an individual entry in the log.
Every time a log entry is made it is prefixed with a string following this pattern:
"4404: 21:42:07.433 - After this point there could be anything (including new line characters and such). However, as soon as the prefix repeats that indicates a new log entry."
4404 Can be any number, but is always then followed by a :.
21:42:07.433 is the 21 hours 42 mins 7 seconds 433 milliseconds.
I don't know much about regex, but is it possible to identify this pattern using it?
I figured something like this would work...
"*: [0-24]:[0:60]:[0:60].[0-1000] - *"
However, it just throws an exception and I fear I'm not on the right track at all.
List<string> split_content = Regex.Matches(file_content, #"*: [0-24]:[0:60]:[0:60].[0-1000] - *").Cast<Match>().Select(m => m.Value).ToList();
The following expression would split a string according to your pattern:
\d+: \d{2}:\d{2}:\d{2}\.\d{3}
Add a ^ in the beginning if your delimiting string always starts a line (and use the m flag for regex). Capturing the log chunks with a regex would be more elaborate, I'd suggest just splitting (with Regex.Split) if you have your log content in the memory all at once.
I've done several syntax highlighting files for simple custom formats in the past (even changing the format a bit to be capable of making the syntax file basing on my skills, in effects).
But this time I feel confused and I will appreciate some help.
The file format is (obviously) a text file where every line contain three distinct elements separated by spaces, they can be "symbols" (names containing a series of alphanumerical chars plus hyphens) or "string" (a series of any chars, spaces included, but not pipes).
Strings can be only at start or end of a line, the middle element can be only a symbol. And string are delimited by a pipe at the end if it is the first element and at the start if it is the last element.
But a line can be also all symbols, string first and rest symbols, and string last and rest symbols.
Strings are always followed by a pipe if they are the first element, or
with a pipe as prefix if they are the last element.
Examples:
All symbols
this-is-a-symbol another-one and-another
First string
This is a string potentially containing any char| symbol symbol
Last string
symbol symbol |A string at the end of the line
First and last as strings
This is a string| now-we-have-a-symbol |And here another string
This four examples are the only possibilities available for a correct formatting.
All symbols need to be colored differently, a specific color for first element, a specific color for second, and one for third.
But strings will have one unique different color regardless of position.
If the pipe chars can be "dimmed" with a color similar (not precisely the same) to background this will be a big plus. But I think I can manage this myself.
A line in the file not like the ones showed will have to be highlighted as an error (like red background).
Some help?
ps: stackoverflow apply a sort of syntax highlighting to my examples which can be misleading
I have found a simpler approach than what I initially thought was necessary in terms of regular expressions. At end I just need to match the first element and the last, how can I've not think of that... So this is my solution, it seems to work well for my specifics. It only doesn't highlight bad formatted lines. Good enough for now. Thanks for the patience and the attention.
" Vim syntax file
" Language: ff .txt
if exists("b:current_syntax")
finish
endif
setlocal iskeyword+=:
syn match Asymbol /^[a-zA-Z0-9\-]* /
syn match Csymbol / [a-zA-Z0-9\-]*$/
syn match Astring /^.*| /
syn match Cstring / |.*$/
highlight link Asymbol Constant
highlight link Csymbol Statement
highlight link Astring Include
highlight link Cstring Comment
let b:current_syntax = "ff"
First, I'm using EditPadPro for my regex cleaning, so any answers given should work within that environment.
I get a large spreadsheet full of data that I have to clean every day. I've managed to get it down to a couple of different regexes that I run, and this works... but I'm curious to see if it's possible to reduce down to a single regex.
Here is some sample data:
3-CPC_114851_70095_70095_CAN-bre
3-CPC_114851_70095_70095_CAN
b11-ao1-113775-bre
b7-ao-114441
b7-ao-114441-bre
b7-ao1-114441
b7-ao1-114441-bre
http://go.nlvid.com/results1/?http://bo
go.nlv/results1/?click
b4-sm-1359
b6-sm-1356-bre
1359_195_1453814569-bre
1356_104_1456856729
b15-rad-8905
b15-rad-8905-bre
Here is how the above data needs to end up:
114851-bre
114851
113775-bre
114441
114441-bre
114441
114441-bre
http://go.nlvid.com/results1/
go.nlv/results1/
sm-1359
sm-1356-bre
sm-1359-bre
sm-1356
rad-8905
rad-8905-bre
So, there are numerous rules, such as:
In cases of more than 2 underscores, the result needs to contain only the value immediately after the first underscore, and everything from the dash onwards.
In cases where the string contains "-ao-", "-ao1-", everything prior to the final numeric string should be removed.
If a question mark is present, everything from the mark onwards should be removed.
If the string contains "-sm-" or "-rad-", everything prior to those alpha strings should be removed.
If the string contains 2 underscores, averything after the first numeric string up to a dash
(if present) should be removed, and the string "sm-" should be prepended.
Additionally there is other data that must be left untouched, including but not limited to:
113535|24905|24905
as well as many variations on this pattern of xxxxxx|yyyyy|zzzzz (and not always those string lengths)
This may be asking way too much of regex, I'm not sure as I'm not great with it. But I've seen some pretty impressive things done with it, so I thought I'd put this out to the community and see what you come back with.
Jonathan, I can wrap all of those into one regex, except the last one (where you prepend sm- to a string that does not contain sm). It is not possible in this context, because we cannot capture "sm" to reuse in the replacement, and because there is no "conditional replacement" syntax in EPP.
That being said, you can achieve what you want in EPP with two regexes and one macro to chain the two.
Here is how.
The solution below is tested in EPP.
Regex 1
Press Ctrl + Sh + F to enter Search / Replace mode
Enter the following Search and Replace in the appropriate boxes
At the top right of the Search bar, click the Favorite Searches pull-down, select "Add", give it a name, e.g. Regex 1
Search:
(?mx)^
(?=(?:[^_\r\n]*?_){3})[^_\r\n]+?_([^_\r\n]+)[^-\r\n]+(-[^\r\n]+)?
|
[^\r\n]*?-ao1?-\D*([^\r\n]+)
|
([^\r\n?]*)(?=\?)[^\r\n]+
|
[^\r\n]*?-((?:sm|rad)-[^\r\n]+)
Replace:
\1\2\3\4\5
Regex 2
Same 1-2-3 steps as above.
Search
^(?!(?:[^_\r\n]*?_){3})(?=(?:[^_\r\n]*?_){2})(\d+)(?:[^-\r\n]+(-[^\r\n]+)?)
Replace
sm-\1\2
Chaining Regex 1 and Regex 2
Top menu: Macros, Record Macro, give it a name.
Click the Favorite searches pulldown, select Regex 1
Hit Replace All.
Click the Favorite searches pulldown, select Regex 2
Hit Replace All.
Macros, Stop recording.
Whenever you want to do your sequence of replacements, pull it by name under the Macros menu.
Testing This
I have tested my "Jonathan macro" on your input. Here is the result:
114851-bre
114851
113775-bre
114441
114441-bre
114441
114441-bre
http://go.nlvid.com/results1/
go.nlv/results1/
sm-1359
sm-1356-bre
sm-1359-bre
sm-1356
rad-8905
rad-8905-bre
Try this:
Toggle the Search Panel : SHIFT+CTRL+F
SEARCH: .*?((?:sm-|rad-)?(?:(?:\d+|[\w\.]+\/.*?))(?:-\w+)?$)
REPLACE: $1
Check REGEX and WORDS
Click Replace All or Hit CTRL+ALT+F3
Check the image below:
I recently discussed editors with a co-worker. He uses one of the less popular editors and I use another (I won't say which ones since it's not relevant and I want to avoid an editor flame war). I was saying that I didn't like his editor as much because it doesn't let you do find/replace with regular expressions.
He said he's never wanted to do that, which was surprising since it's something I find myself doing all the time. However, off the top of my head I wasn't able to come up with more than one or two examples. Can anyone here offer some examples of times when they've found regex find/replace useful in their editor? Here's what I've been able to come up with since then as examples of things that I've actually had to do:
Strip the beginning of a line off of every line in a file that looks like:
Line 25634 :
Line 632157 :
Taking a few dozen files with a standard header which is slightly different for each file and stripping the first 19 lines from all of them all at once.
Piping the result of a MySQL select statement into a text file, then removing all of the formatting junk and reformatting it as a Python dictionary for use in a simple script.
In a CSV file with no escaped commas, replace the first character of the 8th column of each row with a capital A.
Given a bunch of GDB stack traces with lines like
#3 0x080a6d61 in _mvl_set_req_done (req=0x82624a4, result=27158) at ../../mvl/src/mvl_serv.c:850
strip out everything from each line except the function names.
Does anyone else have any real-life examples? The next time this comes up, I'd like to be more prepared to list good examples of why this feature is useful.
Just last week, I used regex find/replace to convert a CSV file to an XML file.
Simple enough to do really, just chop up each field (luckily it didn't have any escaped commas) and push it back out with the appropriate tags in place of the commas.
Regex make it easy to replace whole words using word boundaries.
(\b\w+\b)
So you can replace unwanted words in your file without disturbing words like Scunthorpe
Yesterday I took a create table statement I made for an Oracle table and converted the fields to setString() method calls using JDBC and PreparedStatements. The table's field names were mapped to my class properties, so regex search and replace was the perfect fit.
Create Table text:
...
field_1 VARCHAR2(100) NULL,
field_2 VARCHAR2(10) NULL,
field_3 NUMBER(8) NULL,
field_4 VARCHAR2(100) NULL,
....
My Regex Search:
/([a-z_])+ .*?,?/
My Replacement:
pstmt.setString(1, \1);
The result:
...
pstmt.setString(1, field_1);
pstmt.setString(1, field_2);
pstmt.setString(1, field_3);
pstmt.setString(1, field_4);
....
I then went through and manually set the position int for each call and changed the method to setInt() (and others) where necessary, but that worked handy for me. I actually used it three or four times for similar field to method call conversions.
I like to use regexps to reformat lists of items like this:
int item1
double item2
to
public void item1(int item1){
}
public void item2(double item2){
}
This can be a big time saver.
I use it all the time when someone sends me a list of patient visit numbers in a column (say 100-200) and I need them in a '0000000444','000000004445' format. works wonders for me!
I also use it to pull out email addresses in an email. I send out group emails often and all the bounced returns come back in one email. So, I regex to pull them all out and then drop them into a string var to remove from the database.
I even wrote a little dialog prog to apply regex to my clipboard. It grabs the contents applies the regex and then loads it back into the clipboard.
One thing I use it for in web development all the time is stripping some text of its HTML tags. This might need to be done to sanitize user input for security, or for displaying a preview of a news article. For example, if you have an article with lots of HTML tags for formatting, you can't just do LEFT(article_text,100) + '...' (plus a "read more" link) and render that on a page at the risk of breaking the page by splitting apart an HTML tag.
Also, I've had to strip img tags in database records that link to images that no longer exist. And let's not forget web form validation. If you want to make a user has entered a correct email address (syntactically speaking) into a web form this is about the only way of checking it thoroughly.
I've just pasted a long character sequence into a string literal, and now I want to break it up into a concatenation of shorter string literals so it doesn't wrap. I also want it to be readable, so I want to break only after spaces. I select the whole string (minus the quotation marks) and do an in-selection-only replace-all with this regex:
/.{20,60} /
...and this replacement:
/$0"¶ + "/
...where the pilcrow is an actual newline, and the number of spaces varies from one incident to the next. Result:
String s = "I recently discussed editors with a co-worker. He uses one "
+ "of the less popular editors and I use another (I won't say "
+ "which ones since it's not relevant and I want to avoid an "
+ "editor flame war). I was saying that I didn't like his "
+ "editor as much because it doesn't let you do find/replace "
+ "with regular expressions.";
The first thing I do with any editor is try to figure out it's Regex oddities. I use it all the time. Nothing really crazy, but it's handy when you've got to copy/paste stuff between different types of text - SQL <-> PHP is the one I do most often - and you don't want to fart around making the same change 500 times.
Regex is very handy any time I am trying to replace a value that spans multiple lines. Or when I want to replace a value with something that contains a line break.
I also like that you can match things in a regular expression and not replace the full match using the $# syntax to output the portion of the match you want to maintain.
I agree with you on points 3, 4, and 5 but not necessarily points 1 and 2.
In some cases 1 and 2 are easier to achieve using a anonymous keyboard macro.
By this I mean doing the following:
Position the cursor on the first line
Start a keyboard macro recording
Modify the first line
Position the cursor on the next line
Stop record.
Now all that is needed to modify the next line is to repeat the macro.
I could live with out support for regex but could not live without anonymous keyboard macros.