DefineClones.py - Repertoire clonal assignment toolkit (Python
3)
usage: DefineClones.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}]
[--nproc NPROC] [--sf SEQ_FIELD] [--vf V_FIELD] [--jf J_FIELD] [--gf
GROUP_FIELDS [GROUP_FIELDS ...]] [--mode {allele,gene}] [--act
{first,set}] [--model
{ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}] [--dist
DISTANCE] [--norm {len,mut,none}] [--sym {avg,min}] [--link
{single,average,complete}] [--maxmiss MAX_MISSING]
Assign Ig sequences into clones
- -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)
- --nproc
NPROC
- The number of simultaneous computational processes to execute (CPU cores
to utilized). (default: 8)
- --sf SEQ_FIELD
- Field to be used to calculate distance between records. Defaults to
junction (airr) or JUNCTION (changeo). (default: None)
- --vf V_FIELD
- Field containing the germline V segment call. Defaults to v_call (airr) or
V_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)
- --gf GROUP_FIELDS
[GROUP_FIELDS ...]
- Additional fields to use for grouping clones aside from V, J and junction
length. (default: None)
- --mode
{allele,gene}
- Specifies whether to use the V(D)J allele or gene for initial grouping.
(default: gene)
- --act
{first,set}
- Specifies how to handle multiple V(D)J assignments for initial grouping.
The "first" action will use only the first gene listed. The
"set" action will use all gene assignments and construct a
larger gene grouping composed of any sequences sharing an assignment or
linked to another sequence by a common assignment (similar to
single-linkage). (default: set)
- --model
{ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}
- Specifies which substitution model to use for calculating distance between
sequences. The "ham" model is nucleotide Hamming distance and
"aa" is amino acid Hamming distance. The "hh_s1f" and
"hh_s5f" models are human specific single nucleotide and 5-mer
content models, respectively, from Yaari et al, 2013. The
"mk_rs1nf" and "mk_rs5nf" models are mouse specific
single nucleotide and 5-mer content models, respectively, from Cui et al,
2016. The "m1n_compat" and "hs1f_compat" models are
deprecated models provided backwards compatibility with the
"m1n" and "hs1f" models in Change-O v0.3.3 and SHazaM
v0.1.4. Both 5-mer models should be considered experimental. (default:
ham)
- --dist
DISTANCE
- The distance threshold for clonal grouping (default: 0.0)
- --norm
{len,mut,none}
- Specifies how to normalize distances. One of none (do not normalize), len
(normalize by length), or mut (normalize by number of mutations between
sequences). (default: len)
- --sym {avg,min}
- Specifies how to combine asymmetric distances. One of avg (average of
A->B and B->A) or min (minimum of A->B and B->A). (default:
avg)
- --link
{single,average,complete}
- Type of linkage to use for hierarchical clustering. (default: single)
- --maxmiss
MAX_MISSING
- The maximum number of non-ACGT characters (gaps or Ns) to permit in the
junction sequence before excluding the record from clonal assignment.
Note, under single linkage non-informative positions can create
artifactual links between unrelated sequences. Use with caution. (default:
0)
- clone-pass
- database with assigned clonal group numbers.
- clone-fail
- database with records failing clonal grouping.
- sequence_id, v_call, j_call, junction
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.