SangerAlignment error

[wbooker]

Hi,

I get this error when trying to create an alignment (I only have forward reads). It seems to sort through the files fine, but when it gets to the last sample, I get this:

Error in validObject(.Object) : invalid class “SangerAlignment” object: 1: invalid object for slot "contigsConsensus" in class "SangerAlignment": got class "function", should be or extend class "DNAStringORNULL" invalid class “SangerAlignment” object: 2: invalid object for slot "contigsTree" in class "SangerAlignment": got class "NULL", should be or extend class "phylo"

code is: > my_aligned_contigs <- SangerAlignment(parentDirectory = "C:/Users/Will Booker/Downloads/fwdattachedsequences/test/", suffixForwardRegExp = "1.ab1", minReadsNum = 1)

Thanks!

[roblanf]

Hi @wbooker,

Thanks for raising this issue. We'll get it fixed! If there's any chance you can send me your files off-list (https://biology.anu.edu.au/people/academics/robert-lanfear) that would really help. Of course, I'll only use them for fixing this bug!

Rob

[Kuanhao-Chao]

Hi ! @wbooker Thank you for your bug report. I've fixed the bugs! In contig level, you need to have at least two reads in order to do reads alignment (AlignSeqs function in sangeranalyseR).

Your original code: my_aligned_contigs <- SangerAlignment(parentDirectory = "C:/Users/Will Booker/Downloads/fwdattachedsequences/test/", suffixForwardRegExp = "1.ab1", minReadsNum = 1)

In your case, you ran SangerAlignment function which will automatically group reads into 9 contigs and each of them contains only one read. Therefore, the created SangerAlignment will not contain any valid contigs (you need to have at least 2 reads in each contig).

You can run your data in SangerContig level: my_aligned_contigs <- SangerContig(parentDirectory = "C:/Users/Will Booker/Downloads/fwdattachedsequences/test/", suffixForwardRegExp = "1.ab1", minReadsNum = 1)

Let me know whether this is the result that you want or you want single read in each contig in SangerAlignment.

Thank you!

[roblanf]

Hi Howard,

It seems to me that the flag 'minReadsNum' implies that one can override the (very sensible) default to have at least 2 reads per contig.

Can we set it up that way?

Rob

[Kuanhao-Chao]

_Hi @wbooker

Now you can run the following code on your data correctly.

my_aligned_contigs <- SangerAlignment(parentDirectory = "C:/Users/Will Booker/Downloads/fwdattachedsequences/test/", suffixForwardRegExp = "1.ab1", minReadsNum = 1)

In the latest commit, sangeranalyseR allows single read (in forward or reverse direction) in each contig. Please try the code on your data to see if it's the result that you want. Please let me know if you have any questions!

Howard

[wbooker]

It worked! Thanks a bunch.

-Will

On Thu, Jul 9, 2020 at 2:44 PM Kuan-Hao, Chao notifications@github.com wrote:

_Hi @wbooker https://github.com/wbooker

Now you can run the following code on your data correctly.

my_aligned_contigs <- SangerAlignment(parentDirectory = "C:/Users/Will Booker/Downloads/fwdattachedsequences/test/", suffixForwardRegExp = "1.ab1", minReadsNum = 1)

In the latest commit, sangeranalyseR allows single read (in forward or reverse direction) in each contig. Please try the code on your data to see if it's the result that you want. Please let me know if you have any questions!

Howard

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-- Will Booker (he/him) PhD Candidate Florida State University Dept. of Biological Science, Ecology and Evolution Office: BRF 242 Phone: (770) 500-8152