DefineClones.py

NAME

DefineClones.py - Repertoire clonal assignment toolkit (Python 3)

DESCRIPTION

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

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)

--nproc NPROC

The number of simultaneous computational processes to execute (CPU cores to utilized). (default: 8)

cloning arguments:

--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)

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

AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.