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treeio read tree files form nexus format with extra quotation marks #47

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wook2014 opened this issue Mar 2, 2021 · 3 comments
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@wook2014
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wook2014 commented Mar 2, 2021

Dear @GuangchuangYu
I recently use ggtree to process my phylogenetic tree. I obtained the tree file through IQTree and exported the file in nexus format by figtree. But I meet up with a bug with groupOTU which confused me for a long time. I found the reason is that treeio read the qutoation marks in the nexus file which lead to the group information can not match the sequence names in tree object. I am writing to report this problem and I am wondering if the problem can be fixed.
wuke

@GuangchuangYu
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GuangchuangYu commented Mar 3, 2021 via email

@wook2014
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wook2014 commented Mar 4, 2021

pls provide a reproducible example.

I attached one example file here, but this problem does not just appeared here. This file have problem with double quotation marks. I guess this is because NEXUS file format have too much freedom in Taxa block and the error occurs when read information from Taxa block.

treefile.nexus.txt

@GuangchuangYu
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@xiangpin pls test reading the file with read.beast.

@wook2014 you would better provide source code to reproduce the issue of groupOTU which you mentioned previously.

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