NAME

ConvertDb.py - Repertoire clonal assignment toolkit (Python 3)

DESCRIPTION

usage: ConvertDb.py [--version] [-h] ...
Parses tab delimited database files

help:

--version
show program's version number and exit
-h, --help
show this help message and exit

subcommands:

Database operation
airr
Converts input to an AIRR TSV file.
changeo
Converts input into a Change-O TSV file.
fasta
Creates a fasta file from database records.
baseline
Creates a specially formatted fasta file from database records for input into the BASELINe website. The format groups clonally related sequences sequentially, with the germline sequence preceding each clone and denoted by headers starting with ">>".
genbank
Creates files for GenBank/TLS submissions.

output files:

airr
AIRR formatted database files.
changeo
Change-O formatted database files.
sequences
FASTA formatted sequences output from the subcommands fasta and clip.
genbank
feature tables and fasta files containing MiAIRR compliant input for tbl2asn.

required fields:

sequence_id, sequence, sequence_alignment, junction, v_call, d_call, j_call, v_germline_start, v_germline_end, v_sequence_start, v_sequence_end, d_sequence_start, d_sequence_end, j_sequence_start, j_sequence_end

optional fields:

germline_alignment, c_call, clone_id

AUTHOR


This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.