[ChinmayMoghe]

Feature: Parsing phylogenetic trees

#51

What changed ?

Added a new member called phylo - This is to make sure that this module forms a logical grouping for everything related to phylogenetic trees

• Added phylo - phylo provides memory-efficient data structures and algorithms for phylogenetic analysis and inference

Added phylo/src/lib.rs - Implements Scanner, PhyloParser

• Scanner -> Read multi line newick tree files, is an iterator that emits Vec - that represents a single newick tree
• PhyloParser -> Takes in scanner, is an iterator that emits PhyloTree (as per phylo crate)

This PR is to showcase work in progress and for reference, please share any feedback

[LCrossman]

In terms of robust parsing, I looked through some of my trees and there can be unusual characters in the label, for example:
#, ' (as a biochemical symbol) , -, _ is very common, | , space , [, ], and . is also common

characters reserved in the tree format ( : , ) ; could not ever be in the label, because that would break the format (but it is a possible reason why the format might be invalid)

[ChinmayMoghe]

@LCrossman This is helpful, can you share an example of such a tree with unusual labels, this could become a test case against current implementation, current implementation only creates a Vec<u8> including the ; so that it represents a newick tree, and I let downstream lib (phylo) handle parsing of that tree, we could test out some edge cases with this, if there are any.

[LCrossman]

Edge Cases/tests:

Campylobacter tree of genbank labels and branch lengths:
attached file 1403.aln.treefile.txt
1403.aln.treefile.txt

Multitree file of 10 Staph:
attached file RAxML_bootstrap.my_run.txt
RAxML_bootstrap.my_run.txt

Midpoint rooted and fully Bootstrapped final tree of proteins from Staph:
the bootstraps are specified as 83.7/67 which is bootstrapping values from two different models output from a popular treemaking software.

((((((((((((((((sp|A5IV27|RL16_STAA9:0,sp|Q7A461|RL16_STAAN:0):0,sp|Q5HDW5|RL16_STAAC:0):0,sp|Q99S28|RL16_STAAM:0):0,sp|Q2FEP6|RL16_STAA3:0):0,sp|Q2YYQ3|RL16_STAAB:0):0,sp|Q6G778|RL16_STAAS:0):0,sp|Q6GEJ0|RL16_STAAR:0):0,sp|Q2FW13|RL16_STAA8:0):0,sp|A7X5F4|RL16_STAA1:0):0,sp|A6U3W8|RL16_STAA2:0):0,sp|Q7A080|RL16_STAAW:0):1e-06,sp|A6QJ85|RL16_STAAE:1e-06)83.7/67:0.0071479917,sp|B9DM40|RL16_STACT:0.0216542727)0/23:1e-06,sp|Q4L8A7|RL16_STAHJ:1e-06)0/30:1e-06,(sp|Q5HM06|RL16_STAEQ:1e-06,sp|Q8CRG7|RL16_STAES:1e-06)87.4/88:0.0144074702)NA:0.00725453595,sp|Q49ZG1|RL16_STAS1:0.02891080865);

popular program iqtree2 which creates trees we might want to parse says this:

To avoid problems with downstream software (like tree viewers), IQ-Tree (and also other phylogenetic software) checks the names for such potentially interfering characters and substitutes them by underscores . Permitted characters in sequence names are alphanumeric letters, underscores , dash -, dot ., slash \ and vertical bar |. All other characters are substituted, like e.g. hawk's-eye is converted to hawk_s-eye as which it will appear in the tree.