CreateGermlines.py - Repertoire clonal assignment toolkit (Python
3)
usage: CreateGermlines.py [--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]
Reconstructs germline sequences from alignment data
- -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)
- -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)
- germ-pass
- database with assigned germline sequences.
- germ-fail
- database with records failing germline assignment.
- 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
- n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length,
clone_id
- germline_v_call, germline_d_call, germline_j_call, germline_alignment,
germline_alignment_d_mask, germline_alignment_v_region,
germline_regions,
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.