BuildTrees.py1

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