NAME

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

DESCRIPTION

       usage: CreateGermlines.py [--version] [-h] -d DB_FILES [DB_FILES ...]

       [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
              [--outname   OUT_NAME]   [--log  LOG_FILE]  [--failed]  [--format  {airr,changeo}]  -r  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]

       Reconstructs germline sequences from alignment data

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

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

   standard arguments:
       -d DB_FILES [DB_FILES ...]
              A list of tab delimited database files. (default: None)

       -o OUT_FILES [OUT_FILES ...]
              Explicit  output  file  name.  Note,  this argument cannot be used with the --failed, --outdir, or
              --outname arguments. If unspecified,  then  the  output  filename  will  be  based  on  the  input
              filename(s). (default: None)

       --outdir 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)

       --outname 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)

       --log LOG_FILE
              Specify  to  write  verbose  logging  to  a  file. May not be specified with multiple input files.
              (default: None)

       --failed
              If specified create files containing records that fail processing. (default: False)

       --format {airr,changeo}
              Specify input and output format. (default: airr)

   germline construction arguments:
       -r 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)

       -g {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'])

       --cloned
              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)

       --sf SEQ_FIELD
              Field  containing  the  aligned  sequence.  Defaults to sequence_alignment (airr) or SEQUENCE_IMGT
              (changeo).  (default: None)

       --vf V_FIELD
              Field containing the germline V segment call. Defaults  to  v_call  (airr)  or  V_CALL  (changeo).
              (default: None)

       --df D_FIELD
              Field  containing  the  germline  D  segment  call. Defaults to d_call (airr) or D_CALL (changeo).
              (default: None)

       --jf J_FIELD
              Field containing the germline J segment call. Defaults  to  j_call  (airr)  or  J_CALL  (changeo).
              (default: None)

       --cf CLONE_FIELD
              Field  containing  clone  identifiers.  Ignored  if  --cloned  is  not also specified. Defaults to
              clone_id (airr) or CLONE (changeo). (default: None)

   output files:
              germ-pass

              database with assigned germline sequences.

              germ-fail

              database with records failing germline assignment.

   required fields:
              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

   optional fields:
              n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length, clone_id

   output fields:
              germline_v_call,  germline_d_call, germline_j_call, germline_alignment, germline_alignment_d_mask,
              germline_alignment_v_region, germline_regions,

AUTHOR

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

CreateGermlines.py 1.0.1                          October 2020                             CREATEGERMLINES.PY(1)