topic Re: How to delete numbers in brackets from letter- sequences in Discussions

How to delete numbers in brackets from letter- sequences

KarlK — Wed, 27 Sep 2023 15:00:30 GMT

How can I find modified peptide sequences (e.g., SYELPDGQV(+.98)I(+10.98)T(-17.03)IGNER ) in the Jump table when searching the unmodified sequence (SYELPDGQVITIGNER)?

If the search algorithm cannot be modified, is it possible to generate a new column by deleting all number in brackets from the all-letter- sequences?

e.g., entry original column: NLTEE(+.98)LAGLDE(+28.99)T(+10.98)IAK

automatically generating new column with entry: NLTEEMAGLDETIAK

Re: How to delete numbers in brackets from letter- sequences

jthi — Wed, 27 Sep 2023 15:59:18 GMT

You could create new column using Regex or Substitute

Names Default To Here(1);

str1 = "NLTEE(+.98)LAGLDE(+28.99)T(+10.98)IAK";
str2 = "SYELPDGQV(+.98)I(+10.98)T(-17.03)IGNER";

Show(Regex(str1, "[^ABCDEFGHIJKLMNOPQRSTUVWXYZ]", "", GLOBALREPLACE));
Show(Regex(str2, "[^ABCDEFGHIJKLMNOPQRSTUVWXYZ]", "", GLOBALREPLACE));

This assumes that you want to only keep the letters. You can build it for example by using Recode

and you can use regular expressions with search also

Edit:

Better regex is most likely something like this

Names Default To Here(1);

str1 = "NLTEE(+.98)LAGLDE(+28.99)T(+10.98)IAK";
str2 = "SYELPDGQV(+.98)I(+10.98)T(-17.03)IGNER";

res1 = Regex(str1, "\(.*?\)", "", GLOBALREPLACE);
res2 = Regex(str2, "\(.*?\)", "", GLOBALREPLACE);

show(res1, res2);

Re: How to delete numbers in brackets from letter- sequences

jthi — Wed, 27 Sep 2023 15:31:41 GMT

You can also use Substitute

Names Default To Here(1);

str1 = "NLTEE(+.98)LAGLDE(+28.99)T(+10.98)IAK";
str2 = "SYELPDGQV(+.98)I(+10.98)T(-17.03)IGNER";

res1 = Substitute(str1, Items(Get Punctuation Characters(Include Chars("0123456789")), ""), "");
res2 = Substitute(str2, Items(Get Punctuation Characters(Include Chars("0123456789")), ""), "");

or build regex using JMP's text explorer

Do note that this will leave them as separate "words" as it is used for Text Explorer, so you have to remove the spaces, this can be done with Search for example

Re: How to delete numbers in brackets from letter- sequences

KarlK — Thu, 28 Sep 2023 13:01:25 GMT

Thank you very much for your quick and helpful answers