CreateGermlines

Reconstructs germline sequences from alignment data

usage: CreateGermlines [--version] [-h] -d DB_FILES [DB_FILES ...]
                       [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                       [--outname OUT_NAME] [--log LOG_FILE] [--failed]
                       [--format {airr,changeo}] -r REFERENCES
                       [REFERENCES ...]
                       [-g {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...]]
                       [--cloned] [--sf SEQ_FIELD] [--vf V_FIELD]
                       [--df D_FIELD] [--jf J_FIELD] [--cf CLONE_FIELD]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-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.

--log <log_file>

Specify to write verbose logging to a file. May not be specified with multiple input files.

--failed

If specified create files containing records that fail processing.

--format {airr,changeo}

Specify input and output format.

-r <references>

List of folders and/or fasta files (with .fasta, .fna or .fa extension) with germline sequences. When using the default Change-O sequence and coordinate fields, these reference sequences must contain IMGT-numbering spacers (gaps) in the V segment. Alternative numbering schemes, or no numbering, may work for alternative sequence and coordinate definitions that define a valid alignment, but a warning will be issued.

-g {full,dmask,vonly,regions}

Specify type(s) of germlines to include full germline, germline with D segment masked, or germline for V segment only.

--cloned

Specify to create only one germline per clone. Note, if allele calls are ambiguous within a clonal group, this will place the germline call used for the entire clone within the germline_v_call, germline_d_call and germline_j_call fields.

--sf <seq_field>

Field containing the aligned sequence. Defaults to sequence_alignment (airr) or SEQUENCE_IMGT (changeo).

--vf <v_field>

Field containing the germline V segment call. Defaults to v_call (airr) or V_CALL (changeo).

--df <d_field>

Field containing the germline D segment call. Defaults to d_call (airr) or D_CALL (changeo).

--jf <j_field>

Field containing the germline J segment call. Defaults to j_call (airr) or J_CALL (changeo).

--cf <clone_field>

Field containing clone identifiers. Ignored if –cloned is not also specified. Defaults to clone_id (airr) or CLONE (changeo).

output files:
germ-pass

database with assigned germline sequences.

germ-fail

database with records failing germline assignment.

required fields:

sequence_id, sequence_alignment, v_call, d_call, j_call, v_sequence_start, v_sequence_end, v_germline_start, v_germline_end, d_sequence_start, d_sequence_end, d_germline_start, d_germline_end, j_sequence_start, j_sequence_end, j_germline_start, j_germline_end, np1_length, np2_length

optional fields:

n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length, clone_id

output fields:

germline_v_call, germline_d_call, germline_j_call, germline_alignment, germline_alignment_d_mask, germline_alignment_v_region, germline_regions,