BuildTrees.py - Repertoire clonal assignment toolkit (Python
3)
/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
- -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)
- --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
- 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)
- <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
- sequence_id, sequence, sequence_alignment, germline_alignment_d_mask or
germline_alignment, v_call, j_call, clone_id, v_sequence_start
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.