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.