Accessory scripts
accessory_scripts/
holds standalone helpers that surround the pipeline: preparing its inputs, and
summarising or plotting its outputs. They are not installed by
pip install . — run them from the cloned repository with the EEfinder
environment active.
Note
These scripts are companions rather than part of the supported pipeline. Several
of them shell out to tools that are not in env.yml (cd-hit-est, mafft,
getorf from EMBOSS), and the older ones still refer to EEfinder’s former name,
PEVEI, in their help text. Install the extra tools yourself if you need them.
Preparing inputs
bac_retriever.py
Builds the -mt metadata table for a bacterial protein FASTA by querying Entrez
for each accession found in the headers. See
Acquiring databases.
python accessory_scripts/bac_retriever.py -in <proteins.fa> -em <email> -key <api_key>
ictv_ncbi.py
Takes a three-column CSV and returns protein information grouped by viral family, for assembling family-scoped protein sets.
Post-processing elements
get_copies.py
Clusters the elements in a FASTA with cd-hit-est and reformats the cluster
output, so repeated copies of the same integration can be counted.
python accessory_scripts/get_copies.py -in <PREFIX.EEs.fa> -p 4 -m 4000
get_nr_orfs.py
Runs EMBOSS getorf over a FASTA and removes redundant ORFs by clustering the
result — useful for inspecting the coding potential retained by an element.
python accessory_scripts/get_nr_orfs.py -in <PREFIX.EEs.fa> -ms 300 -p 4 -m 4000
CIAling_auto.py
Clusters a FASTA with cd-hit-est and formats the output for downstream
alignment (mafft).
all_tax_to_tsv.py
Takes a list file naming several *.EEs.tax.tsv files (one per assembly) and
concatenates them into a single TSV organised by assembly — the input the
plotting scripts below expect.
python accessory_scripts/all_tax_to_tsv.py -in tax.lst
Plotting
Script |
Produces |
|---|---|
|
Stacked barplots of taxon composition, one per assembly, from a concatenated taxonomy file. |
|
Beeswarm plots of the elements in a |
|
Stacked barplots relating elements to the transposable elements found in their flanking regions. |
|
R/ggplot2 summaries (molecule type, family and genus counts) of a single |
The Python plotting scripts share a common shape: -in for the input table,
-md/--mode to choose the taxonomic level (Family by default, or Order),
-st/--specifictax to restrict the plot to named taxa, and -gt/--groupbytax
to group rare taxa into an others category (default: fewer than 5 elements).
python accessory_scripts/tax_to_barplot.py -in all_taxonomy.tsv -md Family -gt 5
python accessory_scripts/tax_to_beeswarm.py -in PREFIX.EEs.tax.tsv -st Rhabdoviridae Flaviviridae
taxonomy_plots.R reads its input filename from the top of the script — edit
that line to point at your own taxonomy table before running it.