Parsing phylogenetic trees (newick format)
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评估
- 难度
- 4/5
- 预计耗时
- 3-5 天
- 新手友好度
- 45/100
- Issue 类型
- 功能
- 描述清晰度
- 基本清楚
- 活跃度
- 冷清
- 技术栈
- rust
调研方向
The issue asks for a new phylo.rs module that parses Newick strings into a struct and prints them back; the payload names no existing file to edit. Start by reading the Newick examples in the issue body and decide on the node representation. Done means the listed examples, from the unnamed tree through the rooted-on-a-leaf tree, parse and print back equivalently, with tests for each.
由索引模型根据 Issue 内容生成。
描述
Is your feature request related to a problem? Please describe.
Would like to add parsing of newick format just to print the newick in the first place. Newick is described here:https://en.wikipedia.org/wiki/Newick_format. It is possible to get multiple newick trees inside a single file, they each finish with a semicolon. Some trees can have many nodes, the structure is a graph-type with nodes, edges and leaves. There is an XML format that some python programs parse newick into, phyloXML
Describe the solution you'd like
Looking to start a module phylo.rs with a parse of newick into some type of good struct or hashmap in the first place, with just ability to print it out.
Describe alternatives you've considered
There are some newick tree parsers in crates.io but they all seem to be a few years old, for example newick_0.11.0
Additional context
Various types of newick tree to parse: The one below marked as "popular" is the one I've seen much the most often, so we could concentrate on that structure and allow the others if possible. There are multiple nodes.
(,,(,)); no nodes are named
(A,B,(C,D)); leaf nodes are named
(A,B,(C,D)E)F; all nodes are named
(:0.1,:0.2,(:0.3,:0.4):0.5); all but root node have a distance to parent
(:0.1,:0.2,(:0.3,:0.4):0.5):0.0; all have a distance to parent
(A:0.1,B:0.2,(C:0.3,D:0.4):0.5); distances and leaf names (popular)
(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; distances and all names
((B:0.2,(C:0.3,D:0.4)E:0.5)F:0.1)A; a tree rooted on a leaf node (rare)
- 主要语言
- Rust
- 星标
- 38
- 派生
- 15
- 平均合并
- 21 小时 33 分钟
- 30 天内合并 PR
- 2
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- 没有 Dockerfile 或 Docker Compose 文件
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LCrossman/microBioRust 的其他 Issue
-
good first issue
难度 2/5 1-3 小时 新手友好度 75/100
LCrossman/microBioRust#57 ·
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难度 2/5 1-3 小时 新手友好度 68/100
LCrossman/microBioRust#53 · 1 个 reaction ·
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legacy manual annotation format rare error missing last codon in pseudogene after genbank! parse未关闭
难度 3/5 半天 新手友好度 40/100
LCrossman/microBioRust#50 ·
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enhancement help wanted
难度 4/5 3-5 天 新手友好度 25/100
LCrossman/microBioRust#19 ·
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难度 5/5 一周以上 新手友好度 8/100
LCrossman/microBioRust#18 · 1 个 reaction ·
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