NAME

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

DESCRIPTION

       /usr/bin/BuildTrees.py:488: SyntaxWarning: "is" with a literal. Did you mean "=="?

              if germline is "":

       /usr/bin/BuildTrees.py:543: SyntaxWarning: "is" with a literal. Did you mean "=="?

              if ngermline is "":

       /usr/bin/BuildTrees.py:801: SyntaxWarning: "is not" with a literal. Did you mean "!="?

              if regions["cdr3_imgt"] is not "" and regions["cdr3_imgt"] is not None:

       /usr/bin/BuildTrees.py:827: SyntaxWarning: "is not" with a literal. Did you mean "!="?

              elif regions["fwr3_imgt"] is not "" and regions["fwr3_imgt"] is not None:

       usage: BuildTrees.py [--version] [-h] -d DB_FILES [DB_FILES ...]

       [--outdir OUT_DIR] [--outname OUT_NAME] [--log LOG_FILE]
              [--failed]  [--format  {airr,changeo}] [--collapse] [--ncdr3] [--nmask] [--md META_DATA [META_DATA
              ...]]  [--clones TARGET_CLONES [TARGET_CLONES ...]]  [--minseq  MIN_SEQ]  [--sample  SAMPLE_DEPTH]
              [--append  APPEND  [APPEND  ...]]  [--igphyml]  [--nproc  NPROC]  [--clean {none,all}] [--optimize
              {n,r,l,lr,tl,tlr}] [--omega {e,ce,e,e,ce,e,e,ce,ce,ce}] [-t {e,ce}] [--motifs  MOTIFS]  [--hotness
              HOTNESS] [--oformat {tab,txt}] [--nohlp] [--asr ASR]

       Converts TSV files into IgPhyML input files

   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)

       --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)

   sequence processing arguments:
       --collapse
              If specified, collapse identical sequences before exporting to fasta. (default: False)

       --ncdr3
              If specified, remove CDR3 from all sequences.  (default: False)

       --nmask
              If specified, do not attempt to mask split codons.  (default: False)

       --md META_DATA [META_DATA ...]
              List of fields to containing metadata to include in output fasta file sequence headers.  (default:
              None)

       --clones TARGET_CLONES [TARGET_CLONES ...]
              List of clone IDs to output, if specified. (default: None)

       --minseq MIN_SEQ
              Minimum  number  of  data  sequences. Any clones with fewer than the specified number of sequences
              will be excluded. (default: 1)

       --sample SAMPLE_DEPTH
              Depth of reads to be subsampled (before deduplication). (default: -1)

       --append APPEND [APPEND ...]
              List of columns to append to sequence ID to ensure uniqueness. (default: None)

   IgPhyML arguments (see igphyml -h for details):
       --igphyml
              Run IgPhyML on output? (default: False)

       --nproc NPROC
              Number of threads to parallelize IgPhyML across.  (default: 1)

       --clean {none,all}
              Delete intermediate files? none: leave all intermediate files; all: delete all intermediate files.
              (default: none)

       --optimize {n,r,l,lr,tl,tlr}
              Optimize combination of topology (t) branch lengths (l) and parameters (r), or  nothing  (n),  for
              IgPhyML.  (default: lr)

       --omega {e,ce,e,e,ce,e,e,ce,ce,ce}
              Omega  parameters  to  estimate for FWR,CDR respectively: e = estimate, ce = estimate + confidence
              interval (default: e,e)

       -t {e,ce}
              Kappa parameters to estimate: e = estimate, ce = estimate + confidence interval (default: e)

       --motifs MOTIFS
              Which motifs to estimate mutability. (default: WRC_2:0,GYW_0:1,WA_1:2,TW_0:3,SYC_2:4,GRS_0:5)

       --hotness HOTNESS
              Mutability parameters to estimate: e = estimate, ce = estimate  +  confidence  interval  (default:
              e,e,e,e,e,e)

       --oformat {tab,txt}
              IgPhyML output format. (default: tab)

       --nohlp
              Don't run HLP model? (default: False)

       --asr ASR
              Ancestral sequence reconstruction interval (0-1).  (default: -1)

   output files:
              <folder>

              folder containing fasta and partition files for each clone.

              lineages

              successfully processed records.

              lineages-fail

              database records failed processing.

              igphyml-pass

              parameter estimates and lineage trees from running IgPhyML, if specified

   required fields:
              sequence_id,   sequence,   sequence_alignment,  germline_alignment_d_mask  or  germline_alignment,
              v_call, j_call, clone_id, v_sequence_start

AUTHOR

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

BuildTrees.py 1.0.1                               October 2020                                  BUILDTREES.PY(1)