BuildTrees.py

Converts TSV files into IgPhyML input files

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 OMEGA] [-t KAPPA]
                     [--motifs MOTIFS] [--hotness HOTNESS]
                     [--oformat {tab,txt}] [--nohlp] [--asr ASR]

--version: show program’s version number and exit

-h, --help: show this help message and exit

-d <db_files>: A list of tab delimited database files.

--outdir <out_dir>: Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>: Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

--log <log_file>: Specify to write verbose logging to a file. May not be specified with multiple input files.

--failed: If specified create files containing records that fail processing.

--format {airr,changeo}: Output format. Also specifies the input format for tools accepting tab delimited AIRR Rearrangement or Change-O files.

--collapse: If specified, collapse identical sequences before exporting to fasta.

--ncdr3: If specified, remove CDR3 from all sequences.

--nmask: If specified, do not attempt to mask split codons.

--md <meta_data>: List of fields to containing metadata to include in output fasta file sequence headers.

--clones <target_clones>: List of clone IDs to output, if specified.

--minseq <min_seq>: Minimum number of data sequences. Any clones with fewer than the specified number of sequences will be excluded.

--sample <sample_depth>: Depth of reads to be subsampled (before deduplication).

--append <append>: List of columns to append to sequence ID to ensure uniqueness.

--igphyml: Run IgPhyML on output?

--nproc <nproc>: Number of threads to parallelize IgPhyML across.

--clean {none,all}: Delete intermediate files? none: leave all intermediate files; all: delete all intermediate files.

--optimize {n,r,l,lr,tl,tlr}: Optimize combination of topology (t) branch lengths (l) and parameters (r), or nothing (n), for IgPhyML.

--omega <omega>: Omega parameters to estimate for FWR,CDR respectively: e = estimate, ce = estimate + confidence interval, or numeric value

-t <kappa>: Kappa parameters to estimate: e = estimate, ce = estimate + confidence interval, or numeric value

--motifs <motifs>: Which motifs to estimate mutability.

--hotness <hotness>: Mutability parameters to estimate: e = estimate, ce = estimate + confidence interval, or numeric value

--oformat {tab,txt}: IgPhyML output format.

--nohlp: Don’t run HLP model?

--asr <asr>: Ancestral sequence reconstruction interval (0-1).

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