BuildTrees.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.

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

/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

   standardarguments:-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)

   sequenceprocessingarguments:--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)

   IgPhyMLarguments(seeigphyml-hfordetails):--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)

   outputfiles:
              <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

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

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