Example

This documentation aims to be a complete example walk through for the usage of ShadowCaster. It assumes you have successfully gone through the Installation.

Downloading test data

Download and extract the test data repository of ShadowCaster in a suitable location, see here

Software specifications

The results provided in the test data repository were obtained running ShadowCaster with the following software versions.

O.S:

Linux Mint 18.03 (Sylvia)
Package base:

Ubuntu Xenial
Python:

v2.7.15
R:

v3.4.4
Perl:

v5.22.1
mysql:

v5.7.23
Python packages:
 
  • pip v18.0
  • numpy v1.14.3
  • biopython v1.72
  • matplotlib v2.2.2
  • pandas v0.23.0
  • scipy v1.1.0
  • scikit-learn v0.19.1
  • ete3 v3.1.1
R package:
  • cluster v2.0.7-1

Run ShadowCaster

All fasta files are in the shadowcaster-input and proteomes-output folders. The arguments needed in the args.ini file are:

  • query_genome = /home/user/path/to/shadowcaster-input/Rdenitrificans_genome.fasta
  • query_proteome = /home/user/path/to/shadowcaster-input/Rhodanobacter_denitrificans.fasta
  • proteomes_folder = /home/user/path/to/proteomes-output/proteomes/
  • orthomcl_config = /home/user/orthomcl-pipeline/orthomcl.conf
  • blastp26 = Binary file or your command line used of blastp v2.2.26.
  • formatdb26 = Binary file or your command line used of blastall v2.2.26.
  • nuSVM = 0.4

MUST use the full path of the files or directory.

Run ShadowCaster through:

cd $ShadowCaster/bin/
shadowcaster --config_file args.ini

When ShadowCaster has finished the message “ShadowCaster finished” is printed. The program generates a number of files in the output directory (called with the date and time of the running).

Output description

ShadowCaster generates the following files in the output directory.

log.txt:

Contains used parameters
Parametric folder:
 
  • data4mer_chi2.csv Compositional difference measured with chi2 between each gene and the genome based on 4mers .
  • kl_codonUsage.csv Measure compositional difference of codon usage with Kullback-Leibler.
  • plot_aliens.png Plot of the two compositional features.
  • alien_genes.fasta Fasta file with the alien genes identified by one-class support vector machine.
Phylogenetic folder:
 
  • Orthomcl folder contains files of orthologs groups found by OrthoMCL.
  • orthologs_probabilities.csv the probabilities of orthology between the query proteome and each other genome in the phylogenetic shadow.
  • alien_likelihoods.csv The log likelihood calculated for each alien gene found in the parametric component.
  • histogram_alienLikelihoods.png Histogram of likelihoods from alien genes.
  • hgt_candidates.csv List of HGT candidate genes found with the software with their likelihood.
  • shadowcaster_predictions.fasta Fasta file with genes predicted as HGT by ShadowCaster.

A copy of all the output files can be found in the shadowcaster-output folder.