MakeDb¶

Create tab-delimited database file to store sequence alignment information

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

-h, --help¶: show this help message and exit

--version¶: show program’s version number and exit

output files:

db-pass: database of alignment records with functionality information, V and J calls, and a junction region.
db-fail: database with records that fail due to no functionality information (did not pass IMGT), no V call, no J call, or no junction region.

universal output fields:

SEQUENCE_ID, SEQUENCE_INPUT, SEQUENCE_VDJ, SEQUENCE_IMGT, FUNCTIONAL, IN_FRAME, STOP, MUTATED_INVARIANT, INDELS, V_CALL, D_CALL, J_CALL, V_SEQ_START, V_SEQ_LENGTH, D_SEQ_START, D_SEQ_LENGTH, D_GERM_START, D_GERM_LENGTH, J_SEQ_START, J_SEQ_LENGTH, J_GERM_START, J_GERM_LENGTH, JUNCTION_LENGTH, JUNCTION, NP1_LENGTH, NP2_LENGTH, FWR1_IMGT, FWR2_IMGT, FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, CDR3_IMGT

imgt specific output fields:

V_GERM_START_IMGT, V_GERM_LENGTH_IMGT, N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH, P5J_LENGTH, D_FRAME, V_SCORE, V_IDENTITY, J_SCORE, J_IDENTITY,

igblast specific output fields:

V_GERM_START_VDJ, V_GERM_LENGTH_VDJ, V_EVALUE, V_SCORE, V_IDENTITY, V_BTOP, J_EVALUE, J_SCORE, J_IDENTITY, J_BTOP. CDR3_IGBLAST_NT, CDR3_IGBLAST_AA

ihmm specific output fields:

V_GERM_START_VDJ, V_GERM_LENGTH_VDJ, HMM_SCORE

MakeDb igblast¶

Process IgBLAST output.

usage: MakeDb igblast [-h] [--failed] [--delim DELIMITER DELIMITER DELIMITER]
                          [--outdir OUT_DIR] [--outname OUT_NAME] -i
                          ALIGNER_OUTPUTS [ALIGNER_OUTPUTS ...] -r REPO [REPO ...]
                          -s SEQ_FILES [SEQ_FILES ...] [--noparse] [--partial]
                          [--scores] [--regions] [--cdr3]

-h, --help¶: show this help message and exit

--failed¶: If specified create files containing records that fail processing.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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.

-i <aligner_outputs>¶: IgBLAST output files in format 7 with query sequence (IgBLAST argument ‘-outfmt “7 std qseq sseq btop”’).

-r <repo>¶: List of folders and/or fasta files containing IMGT-gapped germline sequences corresponding to the set of germlines used in the IgBLAST alignment.

-s <seq_files>¶: List of input FASTA files (with .fasta, .fna or .fa extension), containing sequences.

--noparse¶: Specify to prevent input sequence headers from being parsed to add new columns to database. Parsing of sequence headers requires headers to be in the pRESTO annotation format, so this should be specified when sequence headers are incompatible with the pRESTO annotation scheme. Note, unrecognized header formats will default to this behavior.

--partial¶: If specified, include incomplete V(D)J alignments in the pass file instead of the fail file.

--scores¶: Specify if alignment score metrics should be included in the output. Adds the V_SCORE, V_IDENTITY, V_EVALUE, V_BTOP, J_SCORE, J_IDENTITY, J_BTOP, and J_EVALUE columns.

--regions¶: Specify if IMGT FWR and CDRs should be included in the output. Adds the FWR1_IMGT, FWR2_IMGT, FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and CDR3_IMGT columns.

--cdr3¶: Specify if the CDR3 sequences generated by IgBLAST should be included in the output. Adds the columns CDR3_IGBLAST_NT and CDR3_IGBLAST_AA. Requires IgBLAST version 1.5 or greater.

MakeDb ihmm¶

Process iHMMune-Align output.

usage: MakeDb ihmm [-h] [--failed] [--delim DELIMITER DELIMITER DELIMITER]
                       [--outdir OUT_DIR] [--outname OUT_NAME] -i ALIGNER_OUTPUTS
                       [ALIGNER_OUTPUTS ...] -r REPO [REPO ...] -s SEQ_FILES
                       [SEQ_FILES ...] [--noparse] [--partial] [--scores]
                       [--regions]

-h, --help¶: show this help message and exit

--failed¶: If specified create files containing records that fail processing.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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.

-i <aligner_outputs>¶: iHMMune-Align output file.

-r <repo>¶: List of folders and/or FASTA files containing IMGT-gapped germline sequences corresponding to the set of germlines used in the IgBLAST alignment.

-s <seq_files>¶: List of input FASTA files (with .fasta, .fna or .fa extension) containing sequences.

--noparse¶: Specify to prevent input sequence headers from being parsed to add new columns to database. Parsing of sequence headers requires headers to be in the pRESTO annotation format, so this should be specified when sequence headers are incompatible with the pRESTO annotation scheme. Note, unrecognized header formats will default to this behavior.

--partial¶: If specified, include incomplete V(D)J alignments in the pass file instead of the fail file.

--scores¶: Specify if alignment score metrics should be included in the output. Adds the path score of the iHMMune-Align hidden Markov model to HMM_SCORE.

--regions¶: Specify if IMGT FWRs and CDRs should be included in the output. Adds the FWR1_IMGT, FWR2_IMGT, FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and CDR3_IMGT columns.

MakeDb imgt¶

Process IMGT/HighV-Quest output: (does not work with V-QUEST).

usage: MakeDb imgt [-h] [--failed] [--delim DELIMITER DELIMITER DELIMITER]
                       [--outdir OUT_DIR] [--outname OUT_NAME]
                       [-i ALIGNER_OUTPUTS [ALIGNER_OUTPUTS ...]]
                       [-s [SEQ_FILES [SEQ_FILES ...]]] [--noparse] [--partial]
                       [--scores] [--regions] [--junction]

-h, --help¶: show this help message and exit

--failed¶: If specified create files containing records that fail processing.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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.

-i <aligner_outputs>¶: Either zipped IMGT output files (.zip or .txz) or a folder containing unzipped IMGT output files (which must include 1_Summary, 2_IMGT-gapped, 3_Nt-sequences, and 6_Junction).

-s <seq_files>¶: List of input FASTA files (with .fasta, .fna or .fa extension) containing sequences.

--noparse¶: Specify to prevent input sequence headers from being parsed to add new columns to database. Parsing of sequence headers requires headers to be in the pRESTO annotation format, so this should be specified when sequence headers are incompatible with the pRESTO annotation scheme. Note, unrecognized header formats will default to this behavior.

--partial¶: If specified, include incomplete V(D)J alignments in the pass file instead of the fail file.

--scores¶: Specify if alignment score metrics should be included in the output. Adds the V_SCORE, V_IDENTITY, J_SCORE and J_IDENTITY.

--regions¶: Specify if IMGT FWRs and CDRs should be included in the output. Adds the FWR1_IMGT, FWR2_IMGT, FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and CDR3_IMGT columns.

--junction¶: Specify if detailed junction fields should be included in the output. Adds the columns N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH, P5J_LENGTH, D_FRAME.