.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH BUILDTREES.PY "1" "October 2020" "BuildTrees.py 1.0.1" "User Commands"
.SH NAME
BuildTrees.py \- Repertoire clonal assignment toolkit (Python 3)
.SH DESCRIPTION
\fI\,/usr/bin/BuildTrees\/\fP.py:488: SyntaxWarning: "is" with a literal. Did you mean "=="?
.IP
if germline is "":
.PP
\fI\,/usr/bin/BuildTrees\/\fP.py:543: SyntaxWarning: "is" with a literal. Did you mean "=="?
.IP
if ngermline is "":
.PP
\fI\,/usr/bin/BuildTrees\/\fP.py:801: SyntaxWarning: "is not" with a literal. Did you mean "!="?
.IP
if regions["cdr3_imgt"] is not "" and regions["cdr3_imgt"] is not None:
.PP
\fI\,/usr/bin/BuildTrees\/\fP.py:827: SyntaxWarning: "is not" with a literal. Did you mean "!="?
.IP
elif regions["fwr3_imgt"] is not "" and regions["fwr3_imgt"] is not None:
.PP
usage: BuildTrees.py [\-\-version] [\-h] \fB\-d\fR DB_FILES [DB_FILES ...]
.TP
[\-\-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]
.PP
Converts TSV files into IgPhyML input files
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "standard arguments:"
.TP
\fB\-d\fR DB_FILES [DB_FILES ...]
A list of tab delimited database files. (default:
None)
.TP
\fB\-\-outdir\fR 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)
.TP
\fB\-\-outname\fR 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)
.TP
\fB\-\-log\fR LOG_FILE
Specify to write verbose logging to a file. May not be
specified with multiple input files. (default: None)
.TP
\fB\-\-failed\fR
If specified create files containing records that fail
processing. (default: False)
.TP
\fB\-\-format\fR {airr,changeo}
Specify input and output format. (default: airr)
.SS "sequence processing arguments:"
.TP
\fB\-\-collapse\fR
If specified, collapse identical sequences before
exporting to fasta. (default: False)
.TP
\fB\-\-ncdr3\fR
If specified, remove CDR3 from all sequences.
(default: False)
.TP
\fB\-\-nmask\fR
If specified, do not attempt to mask split codons.
(default: False)
.TP
\fB\-\-md\fR META_DATA [META_DATA ...]
List of fields to containing metadata to include in
output fasta file sequence headers. (default: None)
.TP
\fB\-\-clones\fR TARGET_CLONES [TARGET_CLONES ...]
List of clone IDs to output, if specified. (default:
None)
.TP
\fB\-\-minseq\fR MIN_SEQ
Minimum number of data sequences. Any clones with
fewer than the specified number of sequences will be
excluded. (default: 1)
.TP
\fB\-\-sample\fR SAMPLE_DEPTH
Depth of reads to be subsampled (before
deduplication). (default: \fB\-1\fR)
.TP
\fB\-\-append\fR APPEND [APPEND ...]
List of columns to append to sequence ID to ensure
uniqueness. (default: None)
.SS "IgPhyML arguments (see igphyml -h for details):"
.TP
\fB\-\-igphyml\fR
Run IgPhyML on output? (default: False)
.TP
\fB\-\-nproc\fR NPROC
Number of threads to parallelize IgPhyML across.
(default: 1)
.TP
\fB\-\-clean\fR {none,all}
Delete intermediate files? none: leave all
intermediate files; all: delete all intermediate
files. (default: none)
.TP
\fB\-\-optimize\fR {n,r,l,lr,tl,tlr}
Optimize combination of topology (t) branch lengths
(l) and parameters (r), or nothing (n), for IgPhyML.
(default: lr)
.TP
\fB\-\-omega\fR {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)
.TP
\fB\-t\fR {e,ce}
Kappa parameters to estimate: e = estimate, ce =
estimate + confidence interval (default: e)
.TP
\fB\-\-motifs\fR 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)
.TP
\fB\-\-hotness\fR HOTNESS
Mutability parameters to estimate: e = estimate, ce =
estimate + confidence interval (default: e,e,e,e,e,e)
.TP
\fB\-\-oformat\fR {tab,txt}
IgPhyML output format. (default: tab)
.TP
\fB\-\-nohlp\fR
Don't run HLP model? (default: False)
.TP
\fB\-\-asr\fR ASR
Ancestral sequence reconstruction interval (0\-1).
(default: \fB\-1\fR)
.SS "output files:"
.IP
<folder>
.IP
folder containing fasta and partition files for each clone.
.IP
lineages
.IP
successfully processed records.
.IP
lineages\-fail
.IP
database records failed processing.
.IP
igphyml\-pass
.IP
parameter estimates and lineage trees from running IgPhyML, if specified
.SS "required fields:"
.IP
sequence_id, sequence, sequence_alignment,
germline_alignment_d_mask or germline_alignment,
v_call, j_call, clone_id, v_sequence_start
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.