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

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

ConvertDb.py 1.0.1                                October 2020                                   CONVERTDB.PY(1)

       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.

   outputfiles:
              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.

   requiredfields:
              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

   optionalfields:
              germline_alignment, c_call, clone_id

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