So I have a Peptide, which is a string of letters, corresponding to aminoacids
Say the peptide is
peptide_sequence = "VEILANDQGNR"
And it has a modification on L at position 4 and R at position 11,
I would like to insert a "<span class=\"modified_aa\"> and </span> before and after those positions at the same time.
Here is what I tried:
My modifications are stored in an array pep_mods of objects modification containing an attribute location with the position, in this case 4 and 11
pep_mods.each do |m|
peptide_sequence.gsub(peptide_sequence[m.position.to_i-1], "<span class=\"mod\">#{#peptide_sequence[m.location.to_i-1]}</span>" )
end
But since there are two modifications after the first insert of the html span tag the positions in the string become all different
How could I achieve what I intend to do? I hope it was clear
You should work backwards- make the modification starting with the last one. That way the index of earlier modifications is unchanged.
You might need to sort the array of indices in reverse order - then you can use the code you currently have.
Floris's answer is correct, but if you want to do it the hard way (O(n^2) instead of O(nlgn)) here is the basic idea.
Instead of relying on gsub you can iterate over the characters checking if each has an index corresponding to one of the modifications. If the index matches, perform the modification. Otherwise, keep the original character.
modified = peptide_sequence.each_with_index
.to_a
.map do |c, i|
pep_mods.each do |m|
if m.location.to_i = i
%Q{<span class="mod">#{c}</span>}
else
c
end
end
end.join('')
Ok, just in case this is helpful for anyone else, this is how I finally did it:
I first converted the peptide sequence to an array :
pep_seq_arr = peptide_sequence.split("")
then used each_with_index as Casey mentioned
pep_seq_arr.each_with_index do |aa, i|
pep_mods.each do |m|
pep_seq_arr[i] = "<span class='mod'>#{aa}</span>" if i == m.location.to_i-1
end
end
and finally joined the array:
pep_seq_arr.join
It was easier than I first thought
Related
I had the task to code the following:
Take a list of integers and returns the value of these numbers added up, but only if they are odd.
Example input: [1,5,3,2]
Output: 9
I did the code below and it worked perfectly.
numbers = [1,5,3,2]
print(numbers)
add_up_the_odds = []
for number in numbers:
if number % 2 == 1:
add_up_the_odds.append(number)
print(add_up_the_odds)
print(sum(add_up_the_odds))
Then I tried to re-code it using function definition / return:
def add_up_the_odds(numbers):
odds = []
for number in range(1,len(numbers)):
if number % 2 == 1:
odds.append(number)
return odds
numbers = [1,5,3,2]
print (sum(odds))
But I couldn’t make it working, anybody can help with that?
Note: I'm going to assume Python 3.x
It looks like you're defining your function, but never calling it.
When the interpreter finishes going through your function definition, the function is now there for you to use - but it never actually executes until you tell it to.
Between the last two lines in your code, you need to call add_up_the_odds() on your numbers array, and assign the result to the odds variable.
i.e. odds = add_up_the_odds(numbers)
I would like to write a snippet in VS Code that writes a "switch" expression (in Javascript), but one where I can define the number of cases.
Currently there is a snippet that produces the outline of a switch expression with 1 case, and allows you to tab into the condition, case name, and the code contained within.
I want to be able to type "switch5" ("5" being any number) and a switch with 5 cases to be created, where I can tab through the relevant code within.
I know the snippets are written in a JSON file, can I include such conditional logic in this, or is it not possible?
Thanks!
The short answer is that you cannot do that kind of thing in a standard vscode snippet because it cannot dynamically evaluate any input outside of its designated variables with some limited workarounds like I'll mention next.
You might - I and others have written answers on SO about his - type your various case values first and then trigger a snippet tat would transform them into a switch statement. It is sort of doing it backwords but it might be possible.
There are extensions, however, that do allow you to evaluate javascript right in a snippet or setting and output the result. macro-commander is one such extension. I'll show another simpler extension doing what you want: HyperSnips.
In your javascript.hsnips:
snippet `switch(\d)` "add number of cases to a switch statement" A
``
let numCases = Number(m[1]) // 'm' is an array of regex capture groups
let caseString = ''
if (numCases) { // if not 'switch0'
let tabStopNum = 1
caseString = `switch (\${${tabStopNum++}:key}) {\n`
for (let index = 0; index < m[1]; index++) {
caseString += `\tcase \${${tabStopNum++}:value}:\n\t\t\$${tabStopNum++}\n`
caseString += '\t\tbreak;\n\n'
}
caseString += '\tdefault:\n'
caseString += '\t\tbreak;\n}\n'
}
rv = `${caseString}` // return value
``
endsnippet
The trickiest part was getting the unknown number of tabstops to work correctly. This is how I did it:
\${${tabStopNum++}:key}
which will resolve to ${n:defaultValue} where n gets incremented every time a tabstop is inserted. And :defaultValue is an optional default value to that tabstop. If you don't need a defaultValue just use \$${tabStopNum++} there.
See https://stackoverflow.com/a/62562886/836330 for more info on how to set up HyperSnips.
I'm trying to extract the price from the following HTML.
<td>$75.00/<span class='small font-weight-bold text-
danger'>Piece</span></small> *some more text here* </td>
What is the regex expression to get the number 75.00?
Is it something like:
<td>$*/<span class='small font-weight-bold text-danger'>
The dollar sign is a special character in regex, so you need to escape it with a backslash. Also, you only want to capture digits, so you should use character classes.
<td>\$(\d+[.]\d\d)<span
As the other respondent mentioned, regex changes a bit with each implementing language, so you may have to make some adjustments, but this should get you started.
I think you can go with /[0-9]+\.[0-9]+/.
[0-9] matches a single number. In this example you should get the number 7.
The + afterwards just says that it should look for more then just one number. So [0-9]+ will match with 75. It stops there because the character after 5 is a period.
Said so we will add a period to the regex and make sure it's escaped. A period usually means "every character". By escaping it will just look for a period. So we have /[0-9]+\./ so far.
Next we just to add [0-9]+ so it will find the other number(s) too.
It's important that you don't give it the global-flag like this /[0-9]+\.[0-9]+/g. Unless you want it to find more then just the first number/period-combination.
There is another regex you can use. It uses the parentheses to group the part you're looking for like this: /<td>\$(.+)<span/
It will match everything from <td>$ up to <span. From there you can filter out the group/part you're looking for. See the examples below.
// JavaScript
const text = "<td>$something<span class='small font-weight..."
const regex = /<td>\$(.+)<span/g
const match = regex.exec(text) // this will return an Array
console.log( match[1] ) // prints out "something"
// python
text = "<td>$something<span class='small font-weight..."
regex = re.compile(r"<td>\$(.+)<span")
print( regex.search(text).group(1) ) // prints out "something"
As an alternative you could use a DOMParser.
Wrap your <td> inside a table, use for example querySelector to get your element and get the first node from the childNodes.
That would give you $75.00/.
To remove the $ and the trailing forward slash you could use slice or use a regex like \$(\d+\.\d+) and get the value from capture group 1.
let html = `<table><tr><td>$75.00/<span class='small font-weight-bold text-
danger'>Piece</span></small> *some more text here* </td></tr></table>`;
let parser = new DOMParser();
let doc = parser.parseFromString(html, "text/html");
let result = doc.querySelector("td");
let textContent = result.childNodes.item(0).nodeValue;
console.log(textContent.slice(1, -1));
console.log(textContent.match(/\$(\d+\.\d+)/)[1]);
I have a MySQL database whose keys are of this type:
A_10
A_10A
A_10B
A_101
QAb801
QAc5
QAc25
QAd2993
I would like them to sort first by the alpha portion, then by the numeric portion, just like above. I would like this to be the default sorting of this column.
1) how can I sort as specified above, i.e. write a MySQL function?
2) how can I set this column to use the sorting routine by default?
some constraints that might be helpful: the numeric portion of my ID's never exceeds 100,000. I use this fact in some javascript code to convert my ID's to strings concatenating the non-numeric portion with the (number + 1,000,000). (At the time I had not noticed the variations/subparts as above such as A_10A, A_10B, so I'll have to revamp that part of my code.)
The best way to achieve what you want is to store each part in its own column, and I would strongly recommend to change table structure. If it's impossible, you can try the following:
Create 3 UDFs which returns prefix, numeric part, and postfix of your string. For a better performance they should be native (Mysql, as any other RDMS, is not really good in complex string parsing). Then you can call these functions in ORDER BY clause or in trigger body which validates your column. In any case, it will work slower than if you create 3 columns.
No simple answer that I know of. I had something similar a while back but had to use jQuery to sort it. So what I did was first get the output into an javascript array. Then you may want to insert a zero padding to your numbers. Separate the Alpha from Nummerics using a regex, then reassemble the array:
var zarr = new Array();
for(var i=0; i<val.length; i++){
var chunk = val[i].match(/(\d+|[^\d]+)/g).join(',');
var chunks = chunk.split(",");
for(var s=0; s<chunks.length; s++){
if(isNaN(chunks[s]) == true)
zarr.push(chunks[s]);
else
zarr.push(zeroPad(chunks[s], 5));
}
}
function zeroPad(num,count){
var numZeropad = num + '';
while(numZeropad.length < count) {
numZeropad = "0" + numZeropad;
}
return numZeropad;
}
You'll end up with an array like this:
A_00100
QAb00801
QAc00005
QAc00025
QAd02993
Then you can do a natural sort. I know you may want to do it through straight MySQL but I am not to sure if it does natural sorting.
Good luck!
I'm trying to split an HTML document into its head and body:
my #contentsArray = split( /<\/head>/is, $fileContents, 1);
if( scalar #contentsArray == 2 ){
$bodyContents = $dbh->quote(trim($contentsArray[1]));
$headContents = $dbh->quote(trim($contentsArray[0]) . "</head>");
}
is what i have. $fileContents contains the HTML code. When I run this, it doesn't split. Any one know why?
The third parameter to split is how many results to produce, so if you want to apply the expression only once, you would pass 2.
Note that this does actually limit the number of times the pattern is used to split the string (to one fewer than the number passed), not just limit the number of results returned, so this:
print join ":", split /,/, "a,b,c", 2;
outputs:
a:b,c
not:
a:b
sorry, figured it out. Thought the 1 was how many times it would find the expression not limit the results. Changed to 2 and works.