AssignGenes.py
Assign V(D)J gene annotations
usage: AssignGenes.py [--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.py igblast
Executes igblastn.
usage: AssignGenes.py 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] [--cdb CDB] [--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.
- --cdb <cdb>
Name of the custom C reference in the IgBLAST database folder. If not specified, then a default database name with the form imgt_<organism>_<loci>_c will be used. Note, this argument will be ignored for IgBLAST versions below 1.18.0.
- --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.py igblast-aa
Executes igblastp.
usage: AssignGenes.py 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.