Specific string extraction use Excel, R or Python

Question

[sw.arker]

Hello,

I want to extract some specific strings in csv file, using either excel, R or Python.

for example as below: I want to find string from column A in column B and return in column C with 5 amino acid before and after N; thanks!!

A           B                                                       C
INETTDFR    MHRFLLMLLFPFSDNRPMMFFRSFIVFFFLIFFASNVSSRKQTYVIHT        IVGKINETTDF
            VTTSTKHIVTSLFNSLQTENINDDDFSLPEIHYIYENAMSGFSATLTDDQLDT
            VKNTKGFISAYPDELLSLHTTYSHEFLGLEFGIGLWNETSLSSDVIIGLVDTG
            ISPEHVSFRDTHMTPVPSRWRGSCDEGTNFSSSECNKKIIGASAFYKGYE
            SIVGKINETTDFRSTRDAQGHGTHTASTAAGDIVPKANYFGQAKGLASGM
            RFTSRIAAYKACWALGCASTDVIAAIDRAILDGVDVISLSLGGSSRPFYVDP
            IAIAGFGAMQKNIFVSCSAGNSGPTASTVSNGAPWLMTVAASYTDRTFPAIV
            RIGNRKSLVGSSLYKGKSLKNLPLAFNRTAGEESGAVFCIRDSLKRELVEGK
            IVICLRGASGRTAKGEEVKRSGGAAMLLVSTEAEGEELLADPHVLPAVSLGF
            SDGKTLLNYLAGAANATASVRFRGTAYGATAPMVAAFSSRGPSVAGPEIAKP
            DIAAPGLNILAGWSPFSSPSLLRSDPRRVQFNIISGTSMACPHISGIAALIKSV
            HGDWSPAMIKSAIMTTARITDNRNRPIGDRGAAGAESAATAFAFGAGNVDPT
            RAVDPGLVYDTSTVDYLNYLCSLNYTSERILLFSGTNYTCASNAVVLSPGDLN
            YPSFAVNLVNGANLKTVRYKRTVTNVGSPTCEYMVHVEEPKGVKVRVEPKVL
            KFQKARERLSYTVTYDAEASRNSSSSSFGVLVWICDKYNVRSPIAVTWE

[Devon Ryan]

OK, so what have you tried? This should be pretty straight forward in python or R (no clue about excel).

[zx8754]

Provided example doesn't seem to make sense:

A = INETTDFR

B = ...IGASAFYKGYESIVGKINETTDFRSTRDAQGHGTHTAST...

C = IVGKINETTDF

[sw.arker]

The goal is to extract the string from B (whole protein sequence) according to A (identified peptide sequence window), and output as C but taking additional 5 amino acid before and after N.

[Devon Ryan]

The comment was due to the example not including the 5 amino acids following the matched string (in fact, it didn't even include the entire matched string).

[sw.arker]

the output does not include the entire string A, that's ture. because the aim is to get the sequence window with "N" in the middle and 5 aa in front and 5 aa after. the original identified peptide string A did not provide the uniform peptide sequence window with "N" in the middle. That's what I am trying to get by pulling out the specific sequence window from the original protein sequence.

[Devon Ryan]

Ah, both zx8754 and I misread then. I think we both took N as a variable needle.

[sw.arker]

Sorry for the confusion, the N (asparagine) which is potential glycosylated, and I am trying to get the peptide uniform window with the N in the middle. It makes easier and suitable for pattern analysis.

[Alex Reynolds]

I modified my script to anchor on the residue (or residues) of interest within A. I think it should work but you probably would want to test it, first.

[sw.arker]

thanks! Alex, I will definitely try it. by the way, I just find another complicated way to get it by using excel and regular expression tool, just as my backup ;-)

[pld]

This is a basic programming task, check out the csv module in python.

[sw.arker]

Thanks Alex!!

I will try it and modify it accordingly.

Cheers!

Answer 1

[zx8754]

Using Excel*:

=MID(B1,FIND(A1,B1)+FIND("N",A1)-6,5) & "N" & MID(B1,FIND(A1,B1)+FIND("N",A1),5)

*Don't use Excel :)

[sw.arker]

super!! thanks zx8754, it works. actually I was using small part of the same code in combination of regular expression webtool to accomplish the job ;-)

[sw.arker]

I am a rookie in coding (most excel depending), but more and more I figure out for bigger and complicated task, coding makes it more easier and productive!!

Answer 2

[Guangchuang Yu]

Using R:

getPreceding <- function(A, B, N = 4) {
  x <- regexpr(A, B)
  substring(B, x - N, x + attr(x, "match.length") - 1)
}

A = "INETTDFR"
B = "...IGASAFYKGYESIVGKINETTDFRSTRDAQGHGTHTAST..."
getPreceding(A, B)
# [1] "IVGKINETTDFR"