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Command Line Interface

The command-line interface (CLI) offers two modes: a self-test mode and a run mode.

Table of Contents

Run Mode

This mode is used to predict antibiotic resistance of Mycobacterium tuberculosis. The primary run command has several options:

geno2phenotb run [-h] [--skip-mtbseq] [-p] -i DIR -o DIR
                --sample-id SampleID
                [-d DrugCode]

Options:

  • -h, --help
  • --skip-mtbseq
  • -p, --preprocess
  • -i, --fastq-dir
  • -o, --output
  • --sample-id
  • -d, --drug

Below is a description of each option:

-h, --help

Show the help message and exit.

--skip-mtbseq

Skip the MTBseq step. Precomputed output must be present in the specified FASTQ directory.

-p, --preprocess

Run only the preprocessing steps. The FASTQ reads will be assembled using MTBseq and features extracted. This will skip the prediction.

-i DIR, --fastq-dir DIR

Path to the input directory where the FASTQ files are located.

As input, a directory with FASTQ files is required. The FASTQ files must follow this naming scheme:

[SampleID]_[LibID]_[*]_[Direction].f(ast)q.gz
                    ^- Optional values.
Direction must be one of R1, R2.

-o DIR, --output DIR

Path to the directory where the final output files should be stored.

--sample-id SampleID

SampleID (i.e., ERR/SRR run accession). The ID should match with the ID of the FASTQ files.

-d DrugCode, --drug DrugCode

The drug for which resistance should be predicted. If you want predictions for several drugs, use the argument several times, i.e., --d AMK --d DCS --d STR. If the flag is not set, predictions for all drugs will be performed.

The DrugCode is a 2 / 3 letter code and can be one of:

AMK, CAP, DCS, EMB, ETH, FQ, INH, KAN, PAS, PZA, RIF, STR

Examples

Predict the resistance of the sample (ERR551304) against all drugs:

$ geno2phenotb run -i dir_to_ERR551304/ -o output_dir/ --sample-id ERR551304

Predict only the resistance against AMK and RIF:

$ geno2phenotb run -i dir_to_ERR551304/ -o output_dir/ --sample-id ERR551304 -d AMK -d RIF

Skip the MTBseq steps and use the precomputed output:

$ geno2phenotb run -i dir_to_precomputed/ -o output_dir/ --sample-id ERR551304 --skip-mtbseq

Self-test mode

To check the integrity of the installation and dependencies, a self-test can be executed. It does NOT guarantee that everything is okay, but is strong evidence:

geno2phenotb test [-h] (-f | -c)

The available options for the self-test mode are:

  • -h, --help
  • -f, --fast
  • -c, --complete

Descriptions of the self-test mode options:

-h, --help

Show the help message and exit.

-f, --fast

Fast test of the installation. This will not test the preprocessing / MTBSeq steps.

-c, --complete

Complete test of the installation. This will download ~170 MB from the ENA and start a complete run. Depending on your bandwidth / hardware, this may take a few (5-30) minutes.

Examples

To run the complete test (recommended) run:

$ geno2phenotb test -c