In a perl script, I need to replace several strings. At the moment, I use:
$fasta =~ s/\>[^_]+_([^\/]+)[^\n]+/\>$1/g;
The aim is to format in a FASTA file every sequence name. It works well in my case so I don't need to touch this part. However, it happens that a sequence name appears several times in the file. I must not have at the end twice - or more - the same sequence name. I thus need to have for instance:
seqName1
seqName2
etc.
(instead of seqName, seqName, etc.)
Is this possible to somehow process differently every occurrence automatically? I don't know how many sequence there are, if there are similar names, etc. An idea would be to concatenate a random string at every occurrence for instance, hence my question.
Many thanks.
John perfectly solved it and chepner helped with the smart idea to avoid conflicts, here is the final result:
$fasta =~ s/\>[^_]+_([^\/]+)[^\n]+/
sub {
return '>'.$1.$i++;
}->();
/eg;
Many many thanks.
I was actually trying to do something like this the other day, here's what I came up with
$fasta =~ s/\>[^_]+_([^\/]+)[^\n]+/
sub {
# return random string
}->();
/eg;
the \e modifier interprets the substitution as code, not text. I use an anonymous code ref so that I can return at any point.
Related
I'm trying to change the case of method names for some functions from lowercase_with_underscores to lowerCamelCase for lines that begin with public function get_method_name(). I'm struggling to get this done in a single step.
So far I have used the following
:%s/\(get\)\([a-zA-Z]*\)_\(\w\)/\1\2\u\3/g
However, this only replaces one _ character at a time. What I would like it a search and replace that does something like the following:
Identify all lines containing the string public function [gs]et.
On these lines, perform the following search and replace :s/_\(\w\)/\u\1/g
(
EDIT:
Suppose I have lines get_method_name() and set_method_name($variable_name) and I only want to change the case of the method name and not the variable name, how might I do that? The get_method_name() is more simple of course, but I'd like a solution that works for both in a single command. I've been able to use :%g/public function [gs]et/ . . . as per the solution listed below to solve for the get_method_name() case, but unfortunately not the set_method_name($variable_name) case.
If I've understood you correctly, I don't know why the things you've tried haven't worked but you can use g to perform a normal mode command on lines matchings a pattern.
Your example would be something like:
:%g/public function [gs]et/:s/_\(\w\)/\u\1/g
Update:
To match only the method names, we can use the fact that there will only be method names before the first $, as this looks to be PHP.
To do that, we can use a negative lookbehind, #<!:
:%g/public function [gs]et/:s/\(\$.\+\)\#<!_\(\w\)/\u\2/g
This will look behind #<! for any $ followed by any number of characters and only match _\(\w\) if no $s are found.
Bonus points(?):
To do this for multiple buffers stick a bufdo in front of the %g
You want to use a substitute with an expression (:h sub-replace-expression)
Match the complete string you want to process then pass that string to a second substitute command to actually change the string
:%s/\(get\|set\)\zs_\w\+/\=substitute(submatch(0), '_\([A-Za-z]\)', '\U\1', 'g')
Running the above on
get_method_name($variable_name)
set_method_name($variable_name)
returns
getMethodName($variable_name)
setMethodName($variable_name)
To have vi do replace sad with happy, on all lines, in a file:
:1, $ s/sad/happy/g
(It is the :1, $ before the sed command that instructs vi to execute the command on every line in the file.)
I have an issue while trying to read a member of a list like \\server\directory
The issue comes when I try to get this variable using the lindex command, that proceeds with TCL substitution, so the result is:
\serverdirectory
Then, I think I need to use a regsub command to avoid the backslash substitution, but I did not get the correct proceedure.
An example of what I want should be:
set mistring "\\server\directory"
regsub [appropriate regular expresion here]
puts "mistring: '$mistring'" ==> "mistring: '\\server\directory'"
I have checked some posts around this, and keep the \\ is ok, but I still have problems when trying to keep always a single \ followed by any other character that could come here.
UPDATE: specific example. What I am actually trying to keep is the initial format of an element in a list. The list is received by an outer application. The original code is something like this:
set mytable $__outer_list_received
puts "Table: '$mytable'"
for { set i 0 } { $i < [llength $mitabla] } { incr i } {
set row [lindex $mytable $i]
puts "Row: '$row'"
set elements [lindex $row 0]
puts "Elements: '$elements'"
}
The output of this, in this case is:
Table: '{{
address \\server\directory
filename foo.bar
}}'
Row: '{
address \\server\directory
filename foo.bar
}'
Elements: '
address \\server\directory
filename foo.bar
'
So I try to get the value of address (in this specific case, \\server\directory) in order to write it in a configuration file, keeping the original format and data.
I hope this clarify the problem.
If you don't want substitutions, put the problematic string inside curly braces.
% puts "\\server\directory"
\serverdirectory
and it's not what you want. But
% puts {\\server\directory}
\\server\directory
as you need.
Since this is fundamentally a problem on Windows (and Tcl always treats backslashes in double-quotes as instructions to perform escaping substitutions) you should consider a different approach (otherwise you've got the problem that the backslashes are gone by the time you can apply code to “fix” them). Luckily, you've got two alternatives. The first is to put the string in {braces} to disable substitutions, just like a C# verbatim string literal (but that uses #"this" instead). The second is perhaps more suitable:
set mistring [file nativename "//server/directory"]
That ensures that the platform native directory separator is used on Windows (and nowadays does nothing on other platforms; back when old MacOS9 was supported it was much more magical). Normally, you only need this sort of thing if you are displaying full pathnames to users (usually a bad idea, GUI-wise) or if you are passing the name to some API that doesn't like forward slashes (notably when going as an argument to a program via exec but there are other places where the details leak through, such as if you're using the dde, tcom or twapi packages).
A third, although ugly, option is to double the slashes. \\ instead of \, and \ instead of \, while using double quotes. When the substitution occurs it should give you what you want. Of course, this will not help much if you do the substitution a second time.
Is there an easy way to generate a human-readable inflection list from Hunspell/Aspell dictionary data files?
For example, I'd like to generate the following outputs (for different languages):
...
book, books
book, books, booked, booking
...
go, goes, went, gone, going
...
I looked at the Hunspell/Aspell docs, but couldn't find an API call that would do this.
There is a method that the command line one does, but it doesn't output quite in the format you're looking for. You could also do this manually if you wanted though just by some simple scripting with regex.
The format of for each set of affixes is
TYPE TAG REMOVE REPLACE MATCH
Such that where TAG matches what follows what's behind the /in a given word in the .dicfile, you can do the following (presuming you've already stripped the word of the /...):
if($word =~ /$match$/) $word =~ s/$remove$/$replace/;
Notice the $ there matching the end-of-line/word. Adjust with ^ if it's a prefix.
There are three caveats:
The $match directly from the .aff file is in almost all cases equivalent to standard regex. There are minor variations such that if the match is something like [abc-gh], you'd be better to change it to (a|b|c|-|g|h) or [abcgh-] (hunspell doesn't use hyphen as a metacharacter) otherwise it'll be interpreted as [abcdefgh] (standard regex). For a negated character class, your options are to manually move the - to the end of the expression (e.g. [^a-df] to [^adf-] or to use negative look behinds.
If $replace is 0, then you should change it to an empty string.
If your result ends with /..., you need to reprocess it again because it has a double affix.
Be careful. By my rough calculations, the dictionary I'm working on could have more than 50 million words being formed (and I wouldn't be surprised if it hits beyond 100 million).
I have a txt file with content
$NETS
P3V3_AUX_LGATE; PQ6.8 PU37.2
U335_PIN1; R3328.1 U335.1
$END
need to be updated in this format, and save back to another txt file
$NETS
'P3V3_AUX_LGATE'; PQ6.8 PU37.2
'U335_PIN1'; R3328.1 U335.1
$END
NOTE: number of lines may go up to 10,000 lines
My current solution is to read the txt file line by line, detect the presence of the ";" and newline character and do the changes.
Right now i have a variable that holds ALL the lines, is there other way something like Replace via RegEx to do the changes without looping thru each line, this way i can readily print the result
and follow up question, which one is more efficient?
Try
ResultString = Regex.Replace(SubjectString, "^([^;\r\n]+);", "'$1';", RegexOptions.Multiline)
on your multiline string.
This will find any string (length one or more) at the start of a line up until the first semicolon if there is one and replace it with its quoted equivalent.
It should be more efficient than looping through the string line by line as you're doing now, but if you're in doubt, you'd have to profile it.
You could probably find all the matches using something like \w+; but I don't know how you'd be able to do a replace on that using Regex.Replace to add the 's but keep the original match.
However, if you already have it as one variable, you don't have to read the file again, either you could make your code find all ;s and then find the previous newline for each, or you could use a String.Split on newlines to split the variable you've already got into lines.
And if you want to get it back to one variable you can just use String.Join.
Personally I'd normally use the String.Split (and possibly the String.Join if needed) method, since I think that would make the code easy to read.
I would say Yes! this can be done with Regular expressions. Make sure you got the "multiline" option turned on and craft your regular expression using some capture groups to ease the work.
I can however say this will NOT be the optimal one. Since you mention the amount of lines you could be processing, it seems 'resource wise' smarter to use a streaming approach instead of the in memory approach.
Taking the Regex approach (and this took 15 mins so please don't think this is an optimal solution, just prove it would work)
private static Regex matcher = new Regex(#"^\$NETS\r\n(?<entrytitle>.[^;]*);\s*(?<entryrest>.*)\r\n(?<entrytitle2>.[^;]*);\s*(?<entryrest2>.*)\r\n\$END\r\n", RegexOptions.Compiled | RegexOptions.Multiline);
static void Main(string[] args)
{
string newString = matcher.Replace(ExampleFileContent, new MatchEvaluator(evaluator));
}
static string evaluator(Match m)
{
return String.Format("$NETS\r\n'{0}'; {1}\r\n'{2}'; {3}\r\n$END\r\n",
m.Groups["entrytitle"].Value,
m.Groups["entryrest"].Value,
m.Groups["entrytitle2"].Value,
m.Groups["entryrest2"].Value);
}
Hope this helps,
Intro
I work in a facility where we have microscopes. These guys can be asked to generate 4D movies of a sample: they take e.g. 10 pictures at different Z position, then wait a certain amount of time (next timepoint) and take 10 slices again.
They can be asked to save a file for each slice, and they use an explicit naming pattern, something like 2009-11-03-experiment1-Z07-T42.tif. The file names are numbered to reflect the Z position and the time point
Question
Once you have all these file names, you can use a regex pattern to extract the Z and T value, if you know the backbone pattern of the file name. This I know how to do.
The question I have is: do you know a way to automatically generate regex pattern from the file name list? For instance, there is an awesome tool on the net that does similar thing: txt2re.
What algorithm would you use to parse all the file name list and generate a most likely regex pattern?
There is a Perl module called String::Diff which has the ability to generate a regular expression for two different strings. The example it gives is
my $diff = String::Diff::diff_regexp('this is Perl', 'this is Ruby');
print "$diff\n";
outputs:
this\ is\ (?:Perl|Ruby)
Maybe you could feed pairs of filenames into this kind of thing to get an initial regex. However, this wouldn't give you capturing of numbers etc. so it wouldn't be completely automatic. After getting the diff you would have to hand-edit or do some kind of substitution to get a working final regex.
First of all, you are trying to do this the hard way. I suspect that this may not be impossible but you would have to apply some artificial intelligence techniques and it would be far more complicated than it is worth. Either neural networks or a genetic algorithm system could be trained to recognize the Z numbers and T numbers, assuming that the format of Z[0-9]+ and T[0-9]+ is always used somewhere in the regex.
What I would do with this problem is to write a Python script to process all of the filenames. In this script, I would match twice against the filename, one time looking for Z[0-9]+ and one time looking for T[0-9]+. Each time I would count the matches for Z-numbers and T-numbers.
I would keep four other counters with running totals, two for Z-numbers and two for T-numbers. Each pair would represent the count of filenames with 1 match, and the ones with multiple matches. And I would count the total number of filenames processed.
At the end, I would report as follows:
nnnnnnnnnn filenames processed
Z-numbers matched only once in nnnnnnnnnn filenames.
Z-numbers matched multiple times in nnnnnn filenames.
T-numbers matched only once in nnnnnnnnnn filenames.
T-numbers matched multiple times in nnnnnn filenames.
If you are lucky, there will be no multiple matches at all, and you could use the regexes above to extract your numbers. However, if there are any significant number of multiple matches, you can run the script again with some print statements to show you example filenames that provoke a multiple match. This would tell you whether or not a simple adjustment to the regex might work.
For instance, if you have 23,768 multiple matches on T-numbers, then make the script print every 500th filename with multiple matches, which would give you 47 samples to examine.
Probably something like [ -/.=]T[0-9]+[ -/.=] would be enough to get the multiple matches down to zero, while also giving a one-time match for every filename. Or at worst, [0-9][ -/.=]T[0-9]+[ -/.=]
For Python, see this question about TemplateMaker.