[R] How to extract a specific substring from a string (regular expressions) ? See details inside

[David Winsemius]

That did not work on all three:

 > strapply(x, "[A-Z]{3}[0-9]+")
[[1]]
NULL

[[2]]
[1] "CAA15575"

[[3]]
[1] "CAA17111"

But adding a "_" to the initiation pattern and a period to the  
termination pattern makes it complete:

 > library(gsubfn)
 > strapply(x, "[A-Z_]{3}[0-9.]+")
[[1]]
[1] "YP_177963"

[[2]]
[1] "CAA15575"

[[3]]
[1] "CAA17111.1"

Maybe between the two of you and Jim Holtman, I can eventually learn  
how to use regular expressions.

-- 
David.



On Sep 16, 2009, at 10:14 AM, Henrique Dallazuanna wrote:

> Try this:
>
> library(gsubfn)
> strapply(x, "[A-Z]{3}[0-9]+")
>
> On Wed, Sep 16, 2009 at 10:53 AM, Giulio Di Giovanni
> <perimessaggini at hotmail.com> wrote:
>>
>>
>>
>> Hi all,
>>
>> I have thousands of strings like these ones:
>>
>>
>>
>> "1159_1; YP_177963; PPE FAMILY PROTEIN"
>>
>> "1100_13; SECRETED L-ALANINE DEHYDROGENASE ALD CAA15575"
>>
>> "1141_24; gi;2894249;emb;CAA17111.1; PROBABLE ISOCITRATE  
>> DEHYDROGENASE"
>>
>>
>>
>> and various others..
>>
>>
>>
>> I'm interested to extract the code for the protein (in this  
>> example: YP_177963, CAA15575, CAA17111).
>>
>> I found only one common criterion to identify the protein codes in  
>> ALL my strings:
>>
>> I need a sequence of characters selected in this way:
>>
>>
>>
>> start:
>>
>> the first alphabetic capital letter followed after three characters  
>> by a digit
>>
>>
>>
>> end:
>>
>> the last following digit before a non-digit character, or nothing.
>>
>>
>>
>> Tricky, isn't it?
>>
>> Well, I'm not an expert, and I played a lot with regular  
>> expressions and sub() command with no big results. Also with  
>> substring.location in Hmisc package (but here I don't know how to  
>> use regular expressions).
>>
>> Maybe there are other more useful functions  or maybe is just a  
>> matter to use regular expression in a better way...
>>
>>
>>
>> Can anybody help me?
>>

David Winsemius, MD
Heritage Laboratories
West Hartford, CT