danpal96

TreeNode.img_style current description in docs: > Branch length distance to parent node. Default = 0.0 http://etetoolkit.org/docs/latest/reference/reference_tree.html?highlight=img_style#ete3.TreeNode.img_style

Initial node is ignored when using a list in get_common_ancestor

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Manjaro Linux x86_64 python 3.8.8 ete3 3.1.2 The TreeNode get_common_ancestor method says in its docstring: > Returns the first common ancestor between this node and a given list of 'target_nodes'....

Problem with Chapter 14 Modules in Julia 1.1

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I am using Julia 1.1 in Ubuntu 18.04 and was doing the Exercise 14-1 of the Modules Section in chapter 14. Executing the code: ``` include("wc.jl") using LineCount linecount("wc.jl") ```...

Infinite loop in function extract_reads in metagenome mode when length equals max length

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In the function `extract_reads` when `dna_type == "metagenome"` the while loops checks that: ```python3 length > max(seq_len[s].values()) ``` and: ```python3 length < seq_len[s][key] ``` but there is no case for:...

LCA taxomic classification: minimal example

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Could you provide a minimal example for LCA taxomic classification (diamond db and query sequences) using diamond blastx. I have tested concatenating some genes from different species but it always...

Nonpareil v3.4.1 The `-L` option in the usage output talks about a similarity option (-S) but it is not described in the usage output. ``` -L : Minimum overlapping percentage...

Error when checking dependencies in mdmcleaner makedb

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Installation with conda: python=3.11.3 mdmcleaner=0.8.7 I got the next error when running `mdmcleaner makedb ` ``` You are running the following MDMcleaner command: '/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/bin/mdmcleaner makedb -o mdmcleaner' reading settings from...

Documentation of the pipeline

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Could you add a documentation of the pipeline (maybe a wiki) that describes which programs and algorithms are being used in each step? For example, on step one diamond is...

Contrast of text in dendograms

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Version (Anaconda): drep 3.5.0 pyhdfd78af_0 bioconda First of all, thanks for your work, dRep has been very useful in my work. One thing that could be improved is the use...

Version: `r-gggenomes 1.0.1 r44hc72bb7e_0 conda-forge` `add_sublinks` only works with tibbles. If you use a data.frame it throws an error: ```r gggenomes(emale_genes) %>% add_sublinks(as.data.frame(emale_prot_ava)) + geom_gene() + geom_link() ``` Error: ```...