使用Mathematica在已定义位置的左侧或右侧使用"StringCut" [英] 'StringCut' to the left or right of a defined position using Mathematica
问题描述
在阅读这个问题时，我认为使用StringSplit
On reading this question, I thought the following problem would be simple using StringSplit
给出以下字符串，我想将其剪切"到每个"D"的左侧，使得:
Given the following string, I want to 'cut' it to the left of every "D" such that:
-
我得到一个片段的列表(序列保持不变)
StringJoin @fragments返回原始字符串(但是我是否必须重新排序片段以获得该字符串并不重要).也就是说，每个片段中的顺序很重要，我不想丢失任何字符.
StringJoin@fragments gives back the original string (but is does not matter if I have to reorder the fragments to obtain this). That is, sequence within each fragment is important, and I do not want to lose any characters.
(我感兴趣的示例是一个蛋白质序列(字符串)，其中每个字符都代表一个字母代码的氨基酸.我想获得所有片段的理论列表，这些片段是通过用已知的先裂解的酶处理而获得的"D")
(The example I am interested in is a protein sequence (string) where each character represents an amino acid in one-letter code. I want to obtain the theoretical list of ALL fragments obtained by treating with an enzyme known to split before "D")
str = "MTPDKPSQYDKIEAELQDICNDVLELLDSKGDYFRYLSEVASGDN"
我能想到的最好的方法是使用StringReplace在每个"D"之前插入一个空格，然后使用StringSplit.至少可以这样说，这似乎很尴尬.
The best I can come up with is to insert a space before each "D" using StringReplace and then use StringSplit. This seems quite awkward, to say the least.
frags1 = StringSplit@StringReplace[str, "D" -> " D"]
提供输出:
{"MTP", "DKPSQY", "DKIEAELQ", "DICN", "DVLELL", "DSKG", "DYFRYLSEVASG", "DN"}
，或者使用StringReplacePart:
frags1alt =
StringSplit@StringReplacePart[str, " D", StringPosition[str, "D"]]
最后(更现实的是)，如果我想在"D"之前进行拆分，条件是紧接其之前的残基不是"P"(即，PD，(Pro-Asp)键不被裂解)，我可以这样做如下:
Finally (and more realistically), if I want to split before "D" provided that the residue immediately preceding it is not "P" [ie P-D,(Pro-Asp) bonds are not cleaved], I do it as follows:
StringSplit@StringReplace[str, (x_ /; x != "P") ~~ "D" -> x ~~ " D"]
有没有更优雅的方式?
Is there a more elegant way?
速度不一定是问题.我不太可能处理大于500个字符的字符串.我正在使用Mma 7.
Speed is not necessarily an issue. I am unlikely to be dealing with strings of greater than, say, 500 characters. I am using Mma 7.
更新
我已经添加了生物信息学标签，并且我认为从该领域添加示例可能很有趣.
I have added the bioinformatics tag, and I thought it might be of interest to add an example from that field.
以下内容从 NCBI中导入蛋白质序列(牛血清白蛋白，登录号3336842). eutils 数据库，然后生成(理论上的)<一个href ="http://en.wikipedia.org/wiki/Trypsin" rel ="nofollow noreferrer">胰蛋白酶摘要.我假设如果A1不是"R"，"K"或"P"，则当A1为"R"或"K"时，酶的tripsin会在残基A1-A2之间裂解.如果有人有任何改进建议，请随时提出修改建议.
The following imports a protein sequence (Bovine serum albumin, accession number 3336842) from the NCBI database using eutils and then generates a (theoretical) trypsin digest. I have assumed that the enzyme tripsin cleaves between residues A1-A2 when A1 is either "R" or "K", provided that A2 is not "R", "K" or "P". If anyone has any suggestions for improvements, please feel free to suggest modifications.
使用sakra方法的修改(可能需要删除'?db ='之后的回车符):
Using a modification of sakra's method ( a carriage return after '?db=' possibly needs to be removed):
StringJoin /@
Split[Characters[#],
And @@ Function[x, #1 != x] /@ {"R", "K"} ||
Or @@ Function[xx, #2 == xx] /@ {"R", "K", "P"} &] & @
StringJoin@
Rest@Import[
"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=\
protein&id=3336842&rettype=fasta&retmode=text", "Data"]
我可能使用regex方法(Sasha/WReach)来做同样的事情很困难:
My possibly ham-fisted attempt at using the regex method (Sasha/WReach) to do the same thing:
StringSplit[#, RegularExpression["(?![PKR])(?<=[KR])"]] &@
StringJoin@Rest@Import[...]
输出
{MK,WVTFISLLLLFSSAYSR,GVFRR,<<69>>,CCAADDK,EACFAVEGPK,LVVSTQTALA}
推荐答案
以下是一些替代解决方案:
Here are some alternate solutions:
以任何出现的"D"分隔:
Splitting by any occurrence of "D":
In[18]:= StringJoin /@ Split[Characters["MTPDKPSQYDKIEAELQDICNDVLELLDSKGDYFRYLSEVASGDN"], #2!="D" &]
Out[18]:= {"MTP", "DKPSQY", "DKIEAELQ", "DICN", "DVLELL", "DSKG", "DYFRYLSEVASG", "DN"}
以任何出现的"D"分隔，前提是它前面没有"P":
Splitting by any occurrence of "D" provided it is not preceded by "P":
In[19]:= StringJoin /@ Split[Characters["MTPDKPSQYDKIEAELQDICNDVLELLDSKGDYFRYLSEVASGDN"], #2!="D" || #1=="P" &]
Out[19]:= {"MTPDKPSQY", "DKIEAELQ", "DICN", "DVLELL", "DSKG", "DYFRYLSEVASG", "DN"}
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