CreateGermlines.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.

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

       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

   standardarguments:-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)

   germlineconstructionarguments:-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)

   outputfiles:
              germ-pass

              database with assigned germline sequences.

              germ-fail

              database with records failing germline assignment.

   requiredfields:
              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

   optionalfields:
              n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length, clone_id

   outputfields:
              germline_v_call,  germline_d_call, germline_j_call, germline_alignment, germline_alignment_d_mask,
              germline_alignment_v_region, germline_regions,

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