Barcoding gap

Considering a specific sequence collection (e.g. ITS1 sequences belonging to two Aspergillus species), the barcoding gap corresponds to the difference between the greatest intra-specific distance and the smallest inter-specific distance. It is fundamental to evaluate the ability of a specific barcode to discriminate among closely related species and the existence of a barcoding-gap allows to verify it.

_images/image13.jpg

Supplementary Figure 14: A snapshot of the Barcoding Gap submission mask. In the example, the barcoding gap was inferred on the species Saccharomyces cerevisiae.

In particular, the Barcoding Gap (BG) inference tool requires two information:

  1. Taxon list: the name of the taxon on which the BG will be inferred. To streamline the taxon name search an interactive drop-down menu is available;

  1. Taxon rank: taxonomic rank corresponding to the chosen taxon. Two levels are allowed: species and genus.

A boxplot, comparing intra- and inter- group distances is automatically produced as a png file (Supplementary Figure 15). In the result section are also listed two BG measures:

  • the difference between the mean values of intra-taxon and inter-taxa genetic distance;

  • the minimum inter-taxa and maximum intra-taxon genetic distance.

_images/image14.png

Supplementary Figure 15: The obtained boxplot picture for the measured genetic distances for Saccharomyces cerevisiae.

Galaxy usage

_images/barcoding_gap_home.png

The tool allows to select between genus and species.

_images/barcoding_gap_select.png

A png file is produced as output.

_images/barcoding_gap_output.png

Install on Galaxy

Galaxy is able to automatically solve conda dependecies when a tool is started.

To install the Barcoding Gap tool on Galaxy:

  1. Clone the ITSoneWb repository

    git clone https://github.com/ibiom-cnr/itsonewb.git

  2. Add Barcoding Gap tool entry in the galaxy tool_conf.xml file with your favourite editor:

    <section name="Barcoding Gap" id="barcoding_gap">
    <tool file="/opt/itsonewb/barcoding_gap_wrapper/py3/barcoding_gap_wrapper.xml" />
</section>

  3. Finally restart Galaxy.

Command line usage

Barcoding Gap inference tool can be run as follows:

# python print_bg_may21_py3.py --help
usage: print-bg [-h] -d DISTANCE_FOLDER -f ALL_TAXA_FILE_LIST -n TAXON_NAME -r
                TAXONOMIC_RANK [-F OUT_FOLDER]

print the barcoding gap

optional arguments:
  -h, --help            show this help message and exit
  -d DISTANCE_FOLDER, --distance_folder DISTANCE_FOLDER
                        folder in which are stored the distances in family
                        specific files
  -f ALL_TAXA_FILE_LIST, --all_taxa_file_list ALL_TAXA_FILE_LIST
                        file containing all the taxon list
  -n TAXON_NAME, --taxon_name TAXON_NAME
                        taxon name
  -r TAXONOMIC_RANK, --taxonomic_rank TAXONOMIC_RANK
                        taxonomic_rank
  -F OUT_FOLDER, --out_folder OUT_FOLDER
                        output folder

For example for Aspergillus flavus you have:

# python py3/print_bg_may21_py3.py -d barcoding_gap/data_01022019/family_split -f barcoding_gap/data_01022019/all_taxon_list_and_families.csv -n "Aspergillus flavus" -r species
Aspergillus flavus
barcoding_gap/data_01022019/family_split/Aspergillaceae_distaces.tsv.gz
/root/itsonewb/barcoding_gap_wrapper/venv/lib/python3.8/site-packages/plotnine/ggplot.py:719: PlotnineWarning: Saving 4 x 4 in image.
/root/itsonewb/barcoding_gap_wrapper/venv/lib/python3.8/site-packages/plotnine/ggplot.py:722: PlotnineWarning: Filename:    /root/itsonewb/barcoding_gap_wrapper/Aspergillus flavus_dist_plot.png
/root/itsonewb/barcoding_gap_wrapper/venv/lib/python3.8/site-packages/plotnine/ggplot.py:729: MatplotlibDeprecationWarning: savefig() got   unexpected keyword argument "device" which is no longer supported as of 3.3 and will become an error two minor releases later
['0.27', '-0.44', '/root/itsonewb/barcoding_gap_wrapper/Aspergillus flavus_dist_plot.png']

showing the path of the resulting plot.

In this case, file distances have been downloaded and extracted in a directory named barcoding_gap (see next section).

Note

Distances files can be downloaded here.

Install as standalone tool

The barcoding gap inference tool can be found on the ITSoneWB Github repository.

Download the script:

wget https://raw.githubusercontent.com/ibiom-cnr/itsonewb/master/barcoding_gap_wrapper/py3/print_bg_may21_py3.py

The Barcoding Gap tool dependencies can be installed using conda, thorough its Bioconda channel:

conda create --name barcoding_gap numpy matplotlib pandas plotnine -c conda-forge -c bioconda

The command will create a new virtual environment called barcoding_gap wich can be activated with:

conda activate barcoding_gap

Distances files can be downloaded here.

Download and untar them:

wget http://cloud.recas.ba.infn.it:8080/v1/AUTH_2e1bc341b93f480e9b936112962613d8/ITSoneWB/barcoding_gap.tar.gz

tar xvzf barcoding_gap.tar.gz

Docker usage

The Barcoding Gap inference tool is also packaged as Docker Container, hosted on DockerHub.

You can pull it from DockerHub with the following command:

docker pull ibiomcnr/barcoding-gap

The usage of the barcoding gap tool from the docker container is the same as that described in the section Command line usage, using ``print-bg``as alias to call the script.

Note

Distance files are already included in the Docker Container in the /refdata directory. For this reason the option

In the following we report the command example for Aspergillus Flavus:

# docker run -it -v $PWD/bg:/data ibiomcnr/barcoding-gap print-bg -d /refdata/barcoding_gap/data_01022019/family_split -f /refdata/barcoding_gap/data_01022019/all_taxon_list_and_families.csv -n "Aspergillus flavus" -r species -F /data
Aspergillus flavus
/refdata/barcoding_gap/data_01022019/family_split/Aspergillaceae_distaces.tsv.gz
/opt/conda/envs/barcoding_gap/lib/python3.7/site-packages/plotnine/ggplot.py:721: PlotnineWarning: Saving 4 x 4 in image.
/opt/conda/envs/barcoding_gap/lib/python3.7/site-packages/plotnine/ggplot.py:722: PlotnineWarning: Filename: /data/Aspergillus flavus_dist_plot.png
/opt/conda/envs/barcoding_gap/lib/python3.7/site-packages/plotnine/ggplot.py:729: MatplotlibDeprecationWarning: savefig() got unexpected keyword argument "device" which is no longer supported as of 3.3 and will become an error two minor releases later
['0.27', '-0.44', '/data/Aspergillus flavus_dist_plot.png']

Finally the resulting png file can be found in the host directory $PWD/bg.