DefineClones.py

Assign Ig sequences into clones

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]
--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}

Output format. Also specifies the input format for tools accepting tab delimited AIRR Rearrangement or Change-O files.

--nproc <nproc>

The number of simultaneous computational processes to execute (CPU cores to utilized).

--sf <seq_field>

Field to be used to calculate distance between records. Defaults to junction (airr) or JUNCTION (changeo).

--vf <v_field>

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

--jf <j_field>

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

--gf <group_fields>

Additional fields to use for grouping clones aside from V, J and junction length.

--mode {allele,gene}

Specifies whether to use the V(D)J allele or gene for initial grouping.

--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).

--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.

--dist <distance>

The distance threshold for clonal grouping

--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).

--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).

Type of linkage to use for hierarchical clustering.

--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.

output files:
clone-pass

database with assigned clonal group numbers.

clone-fail

database with records failing clonal grouping.

required fields:

sequence_id, v_call, j_call, junction

output fields:

clone_id