AssignGenes

Assign V(D)J gene annotations

usage: AssignGenes [--version] [-h]  ...
--version

show program’s version number and exit

-h, --help

show this help message and exit

output files:
igblast

Reference alignment results from IgBLAST.

AssignGenes igblast

Executes igblastn.

usage: AssignGenes igblast [--version] [-h] [-o OUT_FILES [OUT_FILES ...]]
                           [--outdir OUT_DIR] [--outname OUT_NAME]
                           [--nproc NPROC] -s SEQ_FILES [SEQ_FILES ...] -b
                           IGDATA
                           [--organism {human,mouse,rabbit,rat,rhesus_monkey}]
                           [--loci {ig,tr}] [--vdb VDB] [--ddb DDB]
                           [--jdb JDB] [--format {blast,airr}]
                           [--exec IGBLAST_EXEC]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-o <out_files>

Explicit output file name. Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--outdir <out_dir>

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

--nproc <nproc>

The number of simultaneous computational processes to execute (CPU cores to utilized).

-s <seq_files>

A list of FASTA files containing sequences to process.

-b <igdata>

IgBLAST database directory (IGDATA).

--organism {human,mouse,rabbit,rat,rhesus_monkey}

Organism name.

--loci {ig,tr}

The receptor type.

--vdb <vdb>

Name of the custom V reference in the IgBLAST database folder. If not specified, then a default database name with the form imgt_<organism>_<loci>_v will be used.

--ddb <ddb>

Name of the custom D reference in the IgBLAST database folder. If not specified, then a default database name with the form imgt_<organism>_<loci>_d will be used.

--jdb <jdb>

Name of the custom J reference in the IgBLAST database folder. If not specified, then a default database name with the form imgt_<organism>_<loci>_j will be used.

--format {blast,airr}

Specify the output format. The “blast” will result in the IgBLAST “-outfmt 7 std qseq sseq btop” output format. Specifying “airr” will output the AIRR TSV format provided by the IgBLAST argument “-outfmt 19”.

--exec <igblast_exec>

Path to the igblastn executable.

AssignGenes igblast-aa

Executes igblastp.

usage: AssignGenes igblast-aa [--version] [-h] [-o OUT_FILES [OUT_FILES ...]]
                              [--outdir OUT_DIR] [--outname OUT_NAME]
                              [--nproc NPROC] -s SEQ_FILES [SEQ_FILES ...] -b
                              IGDATA
                              [--organism {human,mouse,rabbit,rat,rhesus_monkey}]
                              [--loci {ig,tr}] [--vdb VDB]
                              [--exec IGBLAST_EXEC]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-o <out_files>

Explicit output file name. Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--outdir <out_dir>

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

--nproc <nproc>

The number of simultaneous computational processes to execute (CPU cores to utilized).

-s <seq_files>

A list of FASTA files containing sequences to process.

-b <igdata>

IgBLAST database directory (IGDATA).

--organism {human,mouse,rabbit,rat,rhesus_monkey}

Organism name.

--loci {ig,tr}

The receptor type.

--vdb <vdb>

Name of the custom V reference in the IgBLAST database folder. If not specified, then a default database name with the form imgt_aa_<organism>_<loci>_v will be used.

--exec <igblast_exec>

Path to the igblastp executable.