usage: pancake create [-h] [--sequences SEQUENCES [SEQUENCES ...]]
                      [--ids IDS [IDS ...]] [--email EMAIL]
                      [--pan_file PAN_FILE] [--ali [ALI [ALI ...]]]
                      [--min_len MIN_LEN] [--no_self_alignments]
                      [--no_refinement] [--max_ref_len MAX_REF_LEN]
                      [--min_entries MIN_ENTRIES]

optional arguments:
  -h, --help            show this help message and exit
  --sequences SEQUENCES [SEQUENCES ...], -s SEQUENCES [SEQUENCES ...]
                        fasta or multiple fasta file providing input
                        chromosome sequences
  --ids IDS [IDS ...], -i IDS [IDS ...]
                        gi ids of sequences to download from NCBI
  --email EMAIL, -e EMAIL
                        if downloading your sequences via gi ids, please
                        specify your email address; in case of excessive
                        usage, NCBI will attempt to contact a user at the
                        e-mail address provided prior to blocking access to
                        the E-utilities
  --pan_file PAN_FILE, -p PAN_FILE
                        File name of new PanCake Object (DEFAULT=pancake.pan)
  --ali [ALI [ALI ...]], -a [ALI [ALI ...]]
                        pairwise alignments (BLAST or nucmer output) to
                        include in PanCake Object
  --min_len MIN_LEN, -l MIN_LEN
                        minimum length of pairwise alignments to include
                        (DEFUALT=25)
  --no_self_alignments, -nsa
                        if set, skip pairwise alignments between regions on
                        identical chromosomes as input (DEFAULT=False)
  --no_refinement, -nr  if set, no post-processing refinements will be done
                        after inclusion of pairwise alignments (DEFAULT=False)
  --max_ref_len MAX_REF_LEN
                        post processing parameter: maximum length of SF's
                        reference sequence to be treated (DEFAULT=3)
  --min_entries MIN_ENTRIES
                        post processing parameter: minimum count of entries in
                        an SF to be treated (DEFUALT=10)