CreateGermlines.py1

help:

--version

show program's version number and exit

-h, --help

show this help message and exit

standard arguments:

-d DB_FILES [DB_FILES ...]

A list of tab delimited database files. (default: None)

-o OUT_FILES [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). (default: None)

--outdir OUT_DIR

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified. (default: None)

--outname OUT_NAME

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files. (default: None)

--log LOG_FILE

Specify to write verbose logging to a file. May not be specified with multiple input files. (default: None)

--failed

If specified create files containing records that fail processing. (default: False)

--format {airr,changeo}

Specify input and output format. (default: airr)

germline construction arguments:

-r REFERENCES [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. (default: None)

-g {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...]

Specify type(s) of germlines to include full germline, germline with D segment masked, or germline for V segment only. (default: ['dmask'])

--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. (default: False)

--sf SEQ_FIELD

Field containing the aligned sequence. Defaults to sequence_alignment (airr) or SEQUENCE_IMGT (changeo). (default: None)

--vf V_FIELD

Field containing the germline V segment call. Defaults to v_call (airr) or V_CALL (changeo). (default: None)

--df D_FIELD

Field containing the germline D segment call. Defaults to d_call (airr) or D_CALL (changeo). (default: None)

--jf J_FIELD

Field containing the germline J segment call. Defaults to j_call (airr) or J_CALL (changeo). (default: None)

--cf CLONE_FIELD

Field containing clone identifiers. Ignored if --cloned is not also specified. Defaults to clone_id (airr) or CLONE (changeo). (default: None)

output files:

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,