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.

DefineClones.py 1.0.1                             October 2020                                DEFINECLONES.PY(1)