MakeDb.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.

MakeDb.py 1.0.1                                   October 2020                                      MAKEDB.PY(1)

       usage: MakeDb.py [--version] [-h]  ...

       Create tab-delimited database file to store sequence alignment information

   help:--version
              show program's version number and exit

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

   subcommands:
              Aligner used

       igblast
              Process igblastn output.

              igblast-aa

              Process igblastp output.

       imgt   Process IMGT/HighV-Quest output (does not work with V-QUEST).

       ihmm   Process iHMMune-Align output.

   outputfiles:
              db-pass

              database  of  alignment  records  with  functionality  information,  V and J calls, and a junction
              region.

              db-fail

              database with records that fail due to no productivity information, no gene  V  assignment,  no  J
              assignment, or no junction region.

   universaloutputfields:
              sequence_id,  sequence,  sequence_alignment, germline_alignment, rev_comp, productive, stop_codon,
              vj_in_frame,   locus,   v_call,   d_call,   j_call,   junction,   junction_length,    junction_aa,
              v_sequence_start,     v_sequence_end,    v_germline_start,    v_germline_end,    d_sequence_start,
              d_sequence_end,    d_germline_start,     d_germline_end,     j_sequence_start,     j_sequence_end,
              j_germline_start, j_germline_end, np1_length, np2_length, fwr1, fwr2, fwr3, fwr4, cdr1, cdr2, cdr3

   imgtspecificoutputfields:
              n1_length,   n2_length,   p3v_length,   p5d_length,   p3d_length,  p5j_length,  d_frame,  v_score,
              v_identity, d_score, d_identity, j_score, j_identity

   igblastspecificoutputfields:
              v_score,  v_identity,  v_support,  v_cigar,  d_score,  d_identity,  d_support,  d_cigar,  j_score,
              j_identity, j_support, j_cigar

   ihmmspecificoutputfields:
              vdj_score

   10Xspecificoutputfields:
              cell_id,  c_call,  consensus_count,  umi_count,  v_call_10x, d_call_10x, j_call_10x, junction_10x,
              junction_10x_aa

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