ViromeClass

A tool for analysing and classifying genome sequences with viral origin in the FASTA format.

REPLICATION

Install the necessary dependencies in a Linux system with:

git clone https://github.com/cobilab/ViromeClass
cd ViromeClass/src/
./Installation.sh

To download the datasets type

./Download_datasets.sh

To analyse a dataset type

make clean
make
./viromeclass -i sequences.fasta -s -g -c -e -m -t 4

To see the possible analysis options type

./viromeclass -h

This will print the following options:

USAGE: ./viromeclass -t <number_of_threads> -i <input_fasta> -s -g -d <sequence_1> [sequence_n]...

Program options --------------------------------------------------------------------------------------------
-h, --help                      Prints this message
-i, --input                     Set input file (FASTA format).
-o, --output                    Set the output file (tsv format).
-s, --size                      Calculates the size and the normalized size of the sequences.
-g, --gc_content                Calculates the GC content.
-b, --base_percentage           Calculates the percentage of the bases A, C, T, G and other in the sequence.
-c, --compression               Calculates the compressibility of the sequences (Markov models).
-e, --entropy                   Calculates the entropy of the sequences.
-m, --melting                   Calculates the maximum melting temperature.
-x, --experiment                Calculates the compressibility of the sequences (GeCo3).
-j, --jarvis                    Calculates the compressibility of the sequences (JARVIS3).
-d, --distance                  Set a sequence to calculate the distance (several sequences can be set).
-a, --additional_metrics        Calculates additional metrics.
-t, --threads                   Sets the number of threads.
-v, --verbose                   Verbose mode - disables progress bar and prints the results.

To train the ML models and classify the sequences in a dataset type

python3 viromeclass.py -tf sequences_train.fasta -cf sequences_to_classify.fasta

To see the possible classification options type

python3 viromeclass.py -h

This will print the following options:

usage: viromeclass.py [-h] [-tf <training_file>] [-tt <training_file>] [-cf <file_to_classify>] [-ct <file_to_classify>] [-s <position>] [-o <analysis_options>]
                      [-p <number_bases_permutations>] [-b] [-t]

Index

options:
  -h, --help            show this help message and exit
  -tf, --training_fasta <training_file>
                        Input training multi-FASTA file
  -tt, --training_tsv <training_file>
                        Input training TSV file
  -cf, --classification_fasta <file_to_classify>
                        Input FASTA file containing the sequences to be classified
  -ct, --classification_tsv <file_to_classify>
                        Input TSV file containing the sequences to be classified
  -s, --segment <position>
                        Part of the Sequence_id that will become the target feature
  -o, --analysis_options <analysis_options>
                        Options for the execution of the C file. Please surround the options with ""
  -p, --permutations <number_bases_permutations>
                        Add permutations of a certain number of characters
  -b, --balance         Balances the training dataset
  -t, --tuning          Tuning mode

CITATION

On using this software/method please cite:

• pending

ISSUES

For any issue let us know at issues link.

LICENSE

GPL v3.

For more information:

http://www.gnu.org/licenses/gpl-3.0.html