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Select sites and sequences from a serially sampled alignment

License: Other

R 8.67% HTML 7.98% Shell 0.53% Python 79.73% PostScript 2.00% CSS 0.07% Parrot 1.02%

lassie's Introduction

lassie

Longitudinal Antigenic Sites and Sequences from Intrahost Evolution

Longitudinal Antigenic Swarm Selection from Intrahost Evolution

An R package of tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment.

Installation and Getting Started:

Start R, by whatever method you choose.
Type "install.packages('devtools')".
If prompted to compile a required package from source, you can safely decline without ill effects.
Type "devtools::install_github('phraber/lassie').
Type "vignette('lassie')".
Run "?lassie::lassie" to begin reading the documentation.

If the you cannot view the vignette, it is available in PDF format here - https://github.com/phraber/lassie/blob/master/tutorial.pdf

Check out the shiny interface, which runs this code interactively:

https://github.com/phraber/meta-lass/

Legalese

This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration.

All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

Recall that this copyright notice must be accompanied by the appropriate open source license terms and conditions.

This is open source software; you can redistribute it and/or modify it under the terms of the GPL-2.0 License. If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from LANL. Full text of the GPL-2.0 License can be found in the LICENSE file in the main development branch of the repository.

lassie's People

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eclarke sleviyang shawhahnlab

lassie's Issues

weblogo installation

Need to automate installation of weblogo and ensure it is accessible on arbitrary system configurations.

report.variant.frequencies fails for one-variant case

One more for you - we've found that in alignments where all amino acids at a given site are the same across timepoints but different from the transmitted founder, report.variant.frequencies fails. I think I have a fix so I'll put the details in another pull request.

swarmset's is_verbose argument still shown in vignette

The lassie vignette shows this for a swarmset example:

eg.swarmset <- swarmset(eg.swarmtools, is_verbose=FALSE)

But the is_verbose argument was removed in 2c94f44.

seqinr::con(x, "profile")

Computing TF loss may be more efficient in the seqinr::consensus method.

plot.swarmset fails during make.logoplot

Thanks for lassie! I was working through the paper and vignette and found that a few items weren't working for me, so I've made a fork with some possible solutions. I'll submit issues and matching pull requests, so you can have a look and see if you'd like to merge them in.

One problem I had was that plot(eg.swarmset) failed with this error:

Error in paste(c(env, shQuote(command), args), collapse = " ") : 
  promise already under evaluation: recursive default argument reference or earlier problems?

I traced that down to make.logoplot's color_option argument not being specified. It looked to me like the simplest fix was just to provide the option like make.timepoint.logos currently does.

weblogo script not executable when installed from devtools::install_github

After installing lassie with devtools::install_github("phraber/lassie") I found that logo-related things like lassie::make.timepoint.logos(eg.swarmset) failed with a permission denied message. Apparently the zip file that devtools downloads from https://api.github.com/repos/ doesn't have the weblogo Python script marked executable, even though it is executable here in the repository.

vignette is inconsistent with usage

vignette('lassie') suggests this should work, though it does not. Need to update vignette.

a <- swarmtools(aas_file=alignment_file, tf_loss_cutoff=0:5*20)
Warning message:
In set.tf.loss.cutoff(retval, tf_loss_cutoff) :
ERROR in set.tf.loss.cutoff(): Please provide a single numeric value.

timepoint labels

To sort samples by time-point sequenced, assume the labels are sorted lexicographically.
That is, d10 will be sorted before d5 unless the labels use leading 0s, e.g. d05 and d10.
The sample timepoint is a character value rather than numeric because it is used internally for column naming.