Traitar3 – the microbial trait analyzer (for Python3)
NOTE: This Python3 implementation is undergoing active development and could change at any time. Use it at your own risk!
Table of Contents
traitar phenotype <in dir> <sample file> from_nucleotides <out_dir>
will trigger the standard workflow of Traitar, which is to predict open reading frames with Prodigal, annotate the coding sequences provided as nucleotide FASTAs in the <in_dir> for all samples in <sample_file> with Pfam families using HMMer and finally predict phenotypes from the models for the 67 traits.
The sample file has one column for the sample file names and one for the names as specified by the user. You can also specify a grouping of the samples in the third column, which will be shown in the generated plots. The template looks like following - The header row is mandatory; please also take a look at the sample file for the packaged example data:
traitar phenotype <in dir> <sample file> from_genes <out_dir>
assumes that gene prediction has been conducted already externally. In this case analysis will start with the Pfam annotation. If the output directory already exists, Traitar will offer to recompute or resume the individual analysis steps. This option is only available if the process is run interactively.
Traitar can benefit from parallel execution:
-cparameter sets the number of processes used for
hmmerand other subprocesses.
-pparameter sets the number of samples (genomes) processed in parallel.
traitar phenotype <in dir> <sample file> from_nucleotides out_dir -c 2
This requires installing GNU parallel as noted above.
Inspect phenotype classification models
Traitar can be used to inspect the protein families in each phenotype model:
traitar show 'Glucose fermenter'
will show the majority features i.e. the Pfam families that contribute to the assignment of the trait Glucose fermenter with phypat classifier to some genome sequence. Via --predictor the user may specify the classifier (phypat, phypat+PGL).
Run Traitar with packaged sample data
traitar phenotype <traitar_dir>/data/sample_data <traitar_dir>/data/sample_data/samples.txt from_genes <out_dir> -c 2 will trigger phenotyping of Listeria grayi DSM_20601 and Listeria ivanovii WSLC3009. Computation should be done within 5 minutes. You can find out
<traitar_dir> by running
python >>> import traitar >>> traitar.__path__
Traitar provides the gene prediction results in
<out_dir>/gene_prediction, the Pfam annotation in
<out_dir>/pfam_annotation and the phenotype prediction in
The phenotype prediction is summarized in heatmaps individually for the phyletic pattern classifier in
heatmap_phypat.png, for the phylogeny-aware classifier in
heatmap_phypat_ggl.png and for both classifiers combined in
heatmap_comb.png and provide hierarchical clustering dendrograms for phenotypes and the samples.
Phenotype prediction - Tables and flat files
These heatmaps are based on tab separated text files e.g.
predictions_majority-vote_combined.txt. A negative prediction is encoded as 0, a prediction made only by the pure phyletic classifier as 1, one made by the phylogeny-aware classifier by 2 and a prediction supported by both algorithms as 3.
predictions_flat_majority-votes_combined.txt provides a flat version of this table with one prediction per row. The expert user might also want to access the individual results for each algorithm in the respective sub folders
Phenotype-relevant protein families and feature tracks
Traitar will link the protein families and predicted phenotypes. The results can be found in
phypat/feat_gffs and ``phypat+PGL/feat_gffs`. If the user picked the 'from nucleotides' option, Traitar will also generate GFF files that link the genes called by Prodidgal with the important protein families. The phenotype-specific protein family annotations tracks can be visualized via GFF files in a genome browser of choice.
Feature tracks with from_genes option (experimental feature)
If the from_genes option is set, the user may specify gene GFF files via an additional column called gene_gff in the sample file. As gene ids are not consistent across gene GFFs from different sources e.g. img, RefSeq or Prodigal the user needs to specify the origin of the gene gff file via the -g / --gene_gff_type parameter. Still there is no guarantee that this works currently. Using samples_gene_gff.txt as the sample file in the above example will generate phenotype-specific Pfam tracks for the two genomes.
traitar phenotype . samples_gene_gff.txt from_genes traitar_out -g refseq
If you use Traitar in your research, please cite our paper:
From genomes to phenotypes: Traitar, the microbial trait analyzer
Aaron Weimann, Kyra Mooren, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C McHardy
mSystem (2016) doi:10.1101/043315