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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
.TH CONVERTDB.PY "1" "October 2020" "ConvertDb.py 1.0.1" "User Commands"
.SH NAME
ConvertDb.py \- Repertoire clonal assignment toolkit (Python 3)
.SH DESCRIPTION
usage: ConvertDb.py [\-\-version] [\-h] ...
.PP
Parses tab delimited database files
.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
Database operation
.TP
airr
Converts input to an AIRR TSV file.
.TP
changeo
Converts input into a Change\-O TSV file.
.TP
fasta
Creates a fasta file from database records.
.TP
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 ">>".
.TP
genbank
Creates files for GenBank/TLS submissions.
.SS "output files:"
.IP
airr
.IP
AIRR formatted database files.
.IP
changeo
.IP
Change\-O formatted database files.
.IP
sequences
.IP
FASTA formatted sequences output from the subcommands fasta and clip.
.IP
genbank
.IP
feature tables and fasta files containing MiAIRR compliant input for tbl2asn.
.SS "required fields:"
.IP
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
.SS "optional fields:"
.IP
germline_alignment, c_call, clone_id
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
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