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.