Provided by: changeo_1.3.0-1_all 

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)