.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH CREATEGERMLINES.PY "1" "October 2020" "CreateGermlines.py 1.0.1" "User Commands"
.SH NAME
CreateGermlines.py \- Repertoire clonal assignment toolkit (Python 3)
.SH DESCRIPTION
usage: CreateGermlines.py [\-\-version] [\-h] \fB\-d\fR DB_FILES [DB_FILES ...]
.TP
[\-o OUT_FILES [OUT_FILES ...]] [\-\-outdir OUT_DIR]
[\-\-outname OUT_NAME] [\-\-log LOG_FILE] [\-\-failed]
[\-\-format {airr,changeo}] \fB\-r\fR REFERENCES
[REFERENCES ...]
[\-g {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...]]
[\-\-cloned] [\-\-sf SEQ_FIELD] [\-\-vf V_FIELD]
[\-\-df D_FIELD] [\-\-jf J_FIELD] [\-\-cf CLONE_FIELD]
.PP
Reconstructs germline sequences from alignment data
.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 "standard arguments:"
.TP
\fB\-d\fR DB_FILES [DB_FILES ...]
A list of tab delimited database files. (default:
None)
.TP
\fB\-o\fR OUT_FILES [OUT_FILES ...]
Explicit output file name. Note, this argument cannot
be used with the \fB\-\-failed\fR, \fB\-\-outdir\fR, or \fB\-\-outname\fR
arguments. If unspecified, then the output filename
will be based on the input filename(s). (default:
None)
.TP
\fB\-\-outdir\fR OUT_DIR
Specify to changes the output directory to the
location specified. The input file directory is used
if this is not specified. (default: None)
.TP
\fB\-\-outname\fR OUT_NAME
Changes the prefix of the successfully processed
output file to the string specified. May not be
specified with multiple input files. (default: None)
.TP
\fB\-\-log\fR LOG_FILE
Specify to write verbose logging to a file. May not be
specified with multiple input files. (default: None)
.TP
\fB\-\-failed\fR
If specified create files containing records that fail
processing. (default: False)
.TP
\fB\-\-format\fR {airr,changeo}
Specify input and output format. (default: airr)
.SS "germline construction arguments:"
.TP
\fB\-r\fR REFERENCES [REFERENCES ...]
List of folders and/or fasta files (with .fasta, .fna
or .fa extension) with germline sequences. When using
the default Change\-O sequence and coordinate fields,
these reference sequences must contain IMGT\-numbering
spacers (gaps) in the V segment. Alternative numbering
schemes, or no numbering, may work for alternative
sequence and coordinate definitions that define a
valid alignment, but a warning will be issued.
(default: None)
.TP
\fB\-g\fR {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...]
Specify type(s) of germlines to include full germline,
germline with D segment masked, or germline for V
segment only. (default: ['dmask'])
.TP
\fB\-\-cloned\fR
Specify to create only one germline per clone. Note,
if allele calls are ambiguous within a clonal group,
this will place the germline call used for the entire
clone within the germline_v_call, germline_d_call and
germline_j_call fields. (default: False)
.TP
\fB\-\-sf\fR SEQ_FIELD
Field containing the aligned sequence. Defaults to
sequence_alignment (airr) or SEQUENCE_IMGT (changeo).
(default: None)
.TP
\fB\-\-vf\fR V_FIELD
Field containing the germline V segment call. Defaults
to v_call (airr) or V_CALL (changeo). (default: None)
.TP
\fB\-\-df\fR D_FIELD
Field containing the germline D segment call. Defaults
to d_call (airr) or D_CALL (changeo). (default: None)
.TP
\fB\-\-jf\fR J_FIELD
Field containing the germline J segment call. Defaults
to j_call (airr) or J_CALL (changeo). (default: None)
.TP
\fB\-\-cf\fR CLONE_FIELD
Field containing clone identifiers. Ignored if
\fB\-\-cloned\fR is not also specified. Defaults to clone_id
(airr) or CLONE (changeo). (default: None)
.SS "output files:"
.IP
germ\-pass
.IP
database with assigned germline sequences.
.IP
germ\-fail
.IP
database with records failing germline assignment.
.SS "required fields:"
.IP
sequence_id, sequence_alignment, v_call, d_call, j_call,
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
.SS "optional fields:"
.IP
n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length,
clone_id
.SS "output fields:"
.IP
germline_v_call, germline_d_call, germline_j_call,
germline_alignment, germline_alignment_d_mask,
germline_alignment_v_region, germline_regions,
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.