Package: traitar
Traitar – the microbial trait analyzerTraitar is a software for characterizing microbial samples from
nucleotide or protein sequences. It can accurately phenotype67 diverse
traits.Table of ContentsInstallationBasic usageResultsDockerCiting TraitarInstallationPlease seeINSTALL.mdfor installation instructions.Basic usagetraitar phenotype <in dir>  <sample file> from_nucleotides <out_dir>will trigger the standardworkflowof Traitar, which is to predict open
reading frames with Prodigal, annotate the coding sequences provided as
nucleotide FASTAs in the for all samples in 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:sample_file_name{tab}sample_name{tab}categorysample1_file_name{tab}sample1_name[{tabl}sample_category1]
sample2_file_name{tab}sample2_name[{tabl}sample_category2]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.Parallel usageTraitar can benefit from parallel execution. The-cparameter sets
the number of processes used e.g.-c2for using two processestraitar phenotype <in dir>  <sample file> from_nucleotides out_dir-c2This requires installing GNU parallel as noted above.Inspect phenotype classification modelsTraitar can be used to inspect the protein families in each phenotype
model:traitar show 'Glucose fermenterwill show the majority features i.e. the Pfam families that contribute
to the assignment of the trait Glucose fermenter withphypatclassifier to some genome sequence. Via –predictor the user may specify
the classifier (phypat, phypat+PGL).Run Traitar with packaged sample datatraitar phenotype<traitar_dir>/data/sample_data<traitar_dir>/data/sample_data/samples.txtfrom_genes <out_dir>-c2will trigger phenotyping ofListeria grayi DSM_20601andListeria
ivanovii WSLC3009. Computation should be done within 5 minutes. You can
find out<traitar_dir>by running``` python
python >>> import traitar >>> traitar.path```ResultsTraitar provides the gene prediction results in<out_dir>/gene_prediction, the Pfam annotation in<out_dir>/pfam_annotationand the phenotype prediction
in<out_dir>/phenotypeprediction.HeatmapsThe phenotype prediction is summarized in heatmaps individually for the
phyletic pattern classifier inheatmap_phypat.png, for the
phylogeny-aware classifier inheatmap_phypat_ggl.pngand for both
classifierscombinedinheatmap_comb.pngand provide hierarchical
clustering dendrograms for phenotypes and the samples.Phenotype prediction - Tables and flat filesThese 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.txtprovides 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 foldersphypatandphypat+PGL.Phenotype-relevant protein families and feature tracksTraitar will link the protein families and predicted phenotypes. The
results can be found inphypat/feat_gffsand
`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 withfrom_genesoption (experimental feature)If thefrom_genesoption 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-grefseqDockerThere is a Docker container available for Traitar. Pull bydocker pull aweimann/traitarTo run traitar for the sample data executedocker run-v<traitar_dir>/data/sample_data:/mnt1445e6c01992 bash-c'traitar phenotype /mnt/ /mnt/samples.txt from_nucleotides /mnt/traitar_out',which will take ~30 minutes. Note there is a problem with parallel usage
so -c option is not guaranteed to work. The output will be owned by
root. So currently you still need root access to your machine to inspect
the traitar_out folder.Citing TraitarIf you use Traitar in your research, please cite our preprint:From genomes to phenotypes: Traitar, the microbial trait analyzerAaron Weimann, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C
McHardybioRxiv(2016) doi:10.1101/043315