6. Predict Synopsis¶

The ./metro executable is composed of several inter-related sub commands. Please see ./metro -h for all available options. The synopsis for the sub command predict shows its parameters and their usage. Optional parameters are shown in square brackets.

$ ./ metro predict [-h] --mutationFile MUTATIONFILE \
                              --alleleList ALLELELIST \
                              --outputdir OUTPUTDIR \
                              --outprefix OUTPREFIX \
                              [--kmerLength KMERLENGTH] \
                              [--peptideLength PEPTIDELENGTH] \
                              [--highbind HIGHBIND] \
                              [--lowbind LOWBIND]

This part of the documentation describes options and concepts for ./metro input sub command in more detail. With minimal configuration, the predict sub command enables you to generate prediction files for each mutated sequence identified in the metro run sub command.

6.1 Required Arguments¶

Each of the following arguments are required. Failure to provide a required argument will result in a non-zero exit-code.

--mutationFile MUTATIONFILE [MUTATIONFILE ...]

Input TSV mutation file to process.
type: file

Input file in tsv format. This can be the output of the METRO run command

Example: --mutationFile data/test_Variant.metro.tsv

Required headers: Required header (in any order): - Variant_Classification - Hugo_Symbol - Transcript_ID - WT_Subset_AA_Sequence - Mutated_Subset_AA_Sequence

--outputdir OUTPUTDIR

Path to an output directory.
type: path

This location is where the metro will create all of its output files, also known as the pipeline's working directory. If the provided output directory does not exist, it will be created automatically.

Example: --outputdir /scratch/$USER/RNA_hg38

--outputprefix OUTPUTPREFIX

Output file prefix.
type: prefix

Prefix for sample output files.

Example: --outputprefix test

--alleleList ALLELELIST

List of Alleles for netMHCpan input.
type: list

Allele name(s) to input into netMHCpan. If this is a list, each allele is separated by commas and without spaces (max 20 per submission). For full list of alleles is available on netMHC's website

Example: --alleleList H-2-Ld,H-2-Dd,H-2-Kb

6.2 Optional Arguments¶

Each of the following arguments are optional and do not need to be provided. Default values listed in each example will be used, if value not provided.

-h, --help

Display Help.
type: boolean

Shows command's synopsis, help message, and an example command

Example: --help

--kmerLength KMERLENGTH

Length of kmer for netMHC input.
type: numeric

Single value, or list, of the length of peptide sequence used for prediction analysis. If this is a list, each length is separated by a comma and without spaces.

Example: --peptideLength 8,9,10,11

--highbind HIGHBIND

Threshold for identifying STRONG affinity.
type: numeric

Threshold to define binding affinity as "STRONG" for netHMC output. Must be an integer that is lower than --lowbind.

Example: --highbind 0.5

--lowbind LOWBIND

Filter for IMPACT values.
type: numeric

Threshold to define binding affinity as "WEAK" for netHMC output. Must be an integer that is higher than --highbind.

Example: --lowbind 2

6.3 Example¶

Predict the binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs) and perform filtering of output based on user-provided parameters.

# login and load interactive session, as described in Getting Started

### Github
module purge
module load python/3.5

## Docker
singularity shell --bind /data/$USER docker://nciccbr/ccbr_metro_v1.4 nciccbr/ccbr_metro_v1.4

## Command 
./metro predict \
                --mutationFile /scratch/$USER/METRO/test_VAF20_Variant.metro.tsv \
                --alleleList H-2-Ld,H-2-Dd,H-2-Kb \
                --peptideLength 8,9,10,11 \
                --kmerLength 21 \
                --outputDir /scratch/$USER/METRO/ \
                --outprefix test