willpearse / phylogenerator2 Goto Github PK
View Code? Open in Web Editor NEWphyloGenerator 2 - (completely) automated phylogenetics for brave
License: Other
phylogenerator2's Issues
Hulk: define constraint tree when input species names
Gene aliasing...
...is needed, because otherwise things like COI are very hard/impossible to search for (Rhiannon's butterflies!!!)
constraint tree support
Website, videos, guide, etc.
phy_params is not implemented?
I tried the simple_plants demo, and when i turn on phy_params (specifically, bootstrapping) nothing different happens: it just performs a simple ML search.
Searching through the repo, I see no other mention of phy_params other than the demo yaml file, so maybe this is just not yet implemented? I'd diagnose further, but unfortunately have no ruby experience :(
Error in Hawkeye using simple_plants demo
Edited simple plants demo to use hawkeye (bottom line change in important):
jhill1@rheic ~/work/software/phyloGenerator2 $ diff demo/simple_plants_he/params.yml demo/simple_plants/params.yml
16c16
< species: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he/leipzig.txt
---
> species: /home/will/Code/phyloGenerator2/demo/simple_plants/species.txt
19c19
< working_dir: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he
---
> working_dir: /home/will/test
21c21
< email: [email protected]
---
> email: [email protected]
32c32
< ref_file: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he/rbcL_reference.fasta
---
> ref_file: /home/will/Code/phyloGenerator2/demo/simple_plants/rbcL_reference.fasta
40c40
< ref_file: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he/matK_reference.fasta
---
> ref_file: /home/will/Code/phyloGenerator2/demo/simple_plants/matK_reference.fasta
60c60
< hawkeye: true
---
> #hawkeye: true
Gives following error:
jhill1@rheic ~/work/software/phyloGenerator2 $ ruby pG_2.rb demo/simple_plants_he/params.yml
phyloGenerator 2.0-2 DOI: 10.1111/2041-210X.12055
Please *use with caution*; first version!
Will Pearse - [email protected]
- Setup complete...
- - rbcL: 143/182 sequences found
- - matK: 106/182 sequences found
- Download complete...
/home/jhill1/work/software/phyloGenerator2/lib/Hawkeye.rb:40:in `check': undefined local variable or method `verbose' for #<Hawkeye:0x00000002d18b50> (NameError)
from /home/jhill1/work/software/phyloGenerator2/lib/Cap.rb:48:in `block (2 levels) in check'
partitions for ExaML and ExaBayes
Things for Curtis
- preferentially download longer sequences (like pG1 did). It may already do this... check! maybe give an option?...
- check for file problems in reference alignments (run test through MAFFT first?) to avoid blue screen of death
- non-windows friendly log-file names
- HawkEye error - couldn't find a certain thing in the folder (?)
- Check a complete HawkEye run for him too (using demo)
- Exclude downloading certain sequences from a previous pG run
Neater output (sorted folders etc.)
Tests
rogues
To check a given phylogeny, and to identify potentially bad sequences
output log file name has a space in it
Sorry. A hugely minor point but like most nerds I despise the creation of file names with spaces:
pG2_log_19-12-2016 16:25
yuck! Add a hyphen or an underscore instead?
PREDICTS to-do list
- Visualisation of alignment so that similar sequences are next to each other
- phlawd alignment algorithm
- output % coverage for each gene (--> "thirty species for this locus")
- specify the annotations you want to get out of the gene (e.g., NADH and multiple sub-components)
- flag identical sequences (by genbank id) even if only as a warning
- some sort of log file that tells you what has been loaded in and what was done with it]
- Windows doesn't use the same new-line character and that's difficult if you're on one of them
- Allow output option and warn about alignment problems with outgroup in PDF
- Be more explicit about when a new directory is created and when some files are expected
- A wrapper script to pull out the sequences that aren't aligning well, re-align, and give a new alignment
- Hawkeye isn't working for the Leipzig example (for Andy)
Refactor actors so parameters are all in hash
ruby installation issues on linux?
(mafft & raxml already installed / executable. Not sure how pg2 will 'find' my raxml though...)
sudo gem install bio
[sudo] password for ross:
Fetching: bio-1.5.1.gem (100%)
Successfully installed bio-1.5.1
Parsing documentation for bio-1.5.1
Installing ri documentation for bio-1.5.1
Done installing documentation for bio after 8 seconds
1 gem installed
$ ./pG_2.rb ./demo/simple_plants/params.yml
Ignoring escape_utils-1.1.0 because its extensions are not built. Try: gem pristine escape_utils --version 1.1.0
Ignoring executable-hooks-1.3.2 because its extensions are not built. Try: gem pristine executable-hooks --version 1.3.2
Ignoring ffi-1.9.10 because its extensions are not built. Try: gem pristine ffi --version 1.9.10
Ignoring gem-wrappers-1.2.7 because its extensions are not built. Try: gem pristine gem-wrappers --version 1.2.7
/usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- bio (LoadError)
from /usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from /home/ross/workspace/phyloGenerator2/lib/Download.rb:6:in `<top (required)>'
from /home/ross/workspace/phyloGenerator2/lib/Cap.rb:2:in `require_relative'
from /home/ross/workspace/phyloGenerator2/lib/Cap.rb:2:in `<top (required)>'
from ./pG_2.rb:6:in `require_relative'
from ./pG_2.rb:6:in `<main>'
Use ruby from non standard location
Will -- Is is possible to update the shebang in pG_2.rb to #!/usr/bin/env ruby? May work better for people like me that have the handicapped ruby shipped with the OS in /usr/bin and a more current version somewhere else. Thx for a great program btw!
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