.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH MAKEDB.PY "1" "October 2020" "MakeDb.py 1.0.1" "User Commands"
.SH NAME
MakeDb.py \- Repertoire clonal assignment toolkit (Python 3)
.SH DESCRIPTION
usage: MakeDb.py [\-\-version] [\-h]  ...
.PP
Create tab\-delimited database file to store sequence alignment information
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "subcommands:"
.IP
Aligner used
.TP
igblast
Process igblastn output.
.IP
igblast\-aa
.IP
Process igblastp output.
.TP
imgt
Process IMGT/HighV\-Quest output (does not work with V\-QUEST).
.TP
ihmm
Process iHMMune\-Align output.
.SS "output files:"
.IP
db\-pass
.IP
database of alignment records with functionality information,
V and J calls, and a junction region.
.IP
db\-fail
.IP
database with records that fail due to no productivity information,
no gene V assignment, no J assignment, or no junction region.
.SS "universal output fields:"
.IP
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
.SS "imgt specific output fields:"
.IP
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
.SS "igblast specific output fields:"
.IP
v_score, v_identity, v_support, v_cigar,
d_score, d_identity, d_support, d_cigar,
j_score, j_identity, j_support, j_cigar
.SS "ihmm specific output fields:"
.IP
vdj_score
.SS "10X specific output fields:"
.IP
cell_id, c_call, consensus_count, umi_count,
v_call_10x, d_call_10x, j_call_10x,
junction_10x, junction_10x_aa
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.