Question

DECIPHER save alignement in outputs

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matamunee • 0

@matamunee-24131

Last seen 4.3 years ago

Hello,

I need to save a PDF or PNG file for several alignements made in DECIPHER with AlignTranslation. BrowseSeqs() produce nice HTML outputs but cant save it into a PDF. I tried msaPrettyprint() but it requires MsaDNAMultipleAlignement class and DECIPHER produces DNAStringSet.

Is there a way to either convert DNAStringSet to MsaDNAMultipleAlignement or to save BrowseSeqs() output into a PDF?

msa decipher output prettyPrint • 2.1k views

ADD COMMENT • link updated 4.3 years ago by UBod ▴ 300 • written 4.3 years ago by matamunee • 0

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You might be able to convert the html file produced by BrowseSeqs() into a pdf file via your web browser or another tool. You can also export DNAStringSets in FASTA format using writeXStringSet().

ADD REPLY • link 4.3 years ago Erik Wright ▴ 150

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I have around 1000alignements, so manually convert them will be a pain. Plus I would like to save the coloration , that's why I tried msaPrettyPrint(). I tried html to pdf automated conversion with prince but the result is not good for me (sequences can be much wider than A4 format so the resulting pdfs do not display alignement correctly)

I want keep the alignment obtained with AlignTranslation() and then use msaPrettyPrint because the conversion into pdf with LaTeX is very convenient for me

ADD REPLY • link 4.3 years ago matamunee • 0

score 0 · Answer 1 · 2020-09-11

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UBod ▴ 300

@ubodenhofer-5425

Last seen 7 months ago

University of Applied Sciences Upper Au…

The answer is quite simple: you can convert your DNAStringSet object into a DNAMultipleAlignment object in the following way:

## suppose that 's' is a 'DNAStringSet' object
s2 <- DNAMultipleAlignment(s)
msaPrettyPrint(s2)

and then call msaPrettyPrint().

ADD COMMENT • link 4.3 years ago UBod ▴ 300