BuildTrees

Converts TSV files into IgPhyML input files

usage: BuildTrees [--version] [-h] -d DB_FILES [DB_FILES ...]
                  [--outdir OUT_DIR] [--outname OUT_NAME] [--log LOG_FILE]
                  [--failed] [--collapse] [--md META_DATA [META_DATA ...]]
                  [--minseq MIN_SEQ]
--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.

--collapse

If specified, collapse identical sequences before exporting to fasta.

--md <meta_data>

List of fields to containing metadata to include in output fasta file sequence headers.

--minseq <min_seq>

Minimum number of data sequences. Any clones with fewer than the specified number of sequences will be excluded.

output files:
<folder>
folder containing fasta and partition files for each clone.
lineages
successfully processed records.
lineages-fail
database records failed processing.
required fields:
SEQUENCE_ID, SEQUENCE_INPUT, SEQUENCE_IMGT, GERMLINE_IMGT_D_MASK, V_CALL, J_CALL