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

        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)

       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

   standardarguments:-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)

   cloningarguments:--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)

   outputfiles:
              clone-pass

              database with assigned clonal group numbers.

              clone-fail

              database with records failing clonal grouping.

   requiredfields:
              sequence_id, v_call, j_call, junction

   outputfields:
              clone_id

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