extractSequence error "replacement has 1 row, data has 0"

[Huck Thornton]

Hi,

Thanks for your efforts. I tried a different approach and am still having issues with the extractSequence function.

When I run: SwitchList <- extractSequence(SwitchList, pathToOutput = "/t1-data/xxx/", writeToFile=TRUE, removeShortAAseq = TRUE, removeLongAAseq=TRUE, alsoSplitFastaFile=TRUE),

I receive the following error message:

Error in `$<-.data.frame`(`*tmp*`, "toBeTrimmed", value = FALSE) : 

  replacement has 1 row, data has 0

In my global environment window, "SwitchList" is listed as a Large switchAnalyzeRlist (12 elements, 342.3 MB). When I type View(SwitchList), it says name: SwitchList, type: Null, and Value: Pairlist of length 0.

I would very much appreciate help on why I am receiving this error message!

[Huck Thornton]

Hi,

As an update, when I ran the command setting removeShortAAseq = FALSE, removeLongAAseq = FALSE, alsoSplitFastaFile = FALSE, it looks like the command could run. So it seems that for some reason I cannot split the Fasta file. Is there an explanation for why this might be the case?

The command I ran was:

SwitchList <- extractSequence(SwitchList, pathToOutput = "/t1-data/xxx/", writeToFile=TRUE, removeShortAAseq = FALSE, removeLongAAseq= FALSE, alsoSplitFastaFile=FALSE)

[Kristoffer Vitting-Seerup]

Thanks for reaching out and sorry for my slow response.

Which version of IsoformSwitchAnalyzeR are you using?

What is the output when you run this code:
summary(SwitchList)

Cheers

Kristoffer

[Huck Thornton]

Hi,

I am using the latest version of IsoformSwitchAnalyzeR installed from Github. It is 1.13.06.

When I type summary(SwitchList), I receive the following output:

This switchAnalyzeRlist list contains:

 129763 isoforms from 31381 genes

 1 comparison from 2 conditions (in total 6 samples)

Feature analyzed:

[1] "ntSequence"

What should I do next?

[Kristoffer Vitting-Seerup]

That sounds very strange - but I'm afraid I would need the switchAnalyzeRlist to debug this one.

Would you be willing to share your switchAnalyzeRlist - I would naturally keep it confidential and only use it to debug your problem.

If you are willing you can use the save() command to save it and email me (a link). My email can be found at BioC.

Cheers

Kristoffer

[Kristoffer Vitting-Seerup]

Hi Huck

I've had a chance to look at your data and the problem is that the GTF you supply does not have any open reading frame info and unfortunatly I did not check for this problem.

I've pushed IsoformSwitchAnalyzeR 1.13.07 to github which give the right warning.

Thanks for repporting the problem.

Cheers

Kristoffer