mafExtractor would split MSA even they should be together

Question

mafExtractor would split MSA even they should be together

zy041225 opened this issue 7 years ago · 3 comments

Hi,

I'm dealing with my MSA using mafExtractor, but some output is split into two or more alignments when they should be one.

For example, when running the following command
mafExtractor --maf chrX.nonoverlap.maf --seq "hsap.chrX" --start 100067347 --stop 100067714 > split/chrX.nonoverlap.maf.100067347-100067714.maf

one of the MSA
origin.txt

are split into multiple parts
split.txt

and if I add --soft, it output the same alignment as input without extraction

Please check.

Answer 1 · 2017-12-05T15:07:54.000Z

I'm pretty sure it's doing the right thing here. The sequence you asked for, hsap.chrX, has gaps in it. mafExtractor only cares about that sequence so any insertions are left out.

Answer 2 · 2017-12-05T15:28:33.000Z

Thanks for the explanation. BTW, will mafExtractor check if there's any gap in reference only?

Answer 3 · 2017-12-05T17:20:37.000Z

Right, it walks the reference and pulls out all blocks that contain the reference and cuts blocks that lack the reference.

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On Tue, Dec 5, 2017 at 07:28 zy041225 ***@***.***> wrote: Thanks for the explanation. BTW, will mafExtractor check if there's any gap in reference only? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAkV8vYfGR87hJAD7fZv2nuQSGYCHlEHks5s9WEigaJpZM4QlwhN> .