Fetching contributors…
Cannot retrieve contributors at this time
113 lines (88 sloc) 4.64 KB


Something like this:

$ SeqFindr -h

usage: SeqFindr [-h] [-R {nucl,prot}] [-X] [--evalue EVALUE] [--short] [-v]
                [-o OUTPUT] [-p OUTPUT_PREFIX] [-t TOL] [-m CONS] [-l] [-r]
                [-g] [--index_file INDEX_FILE] [--color COLOR] [--DPI DPI]
                [--seed SEED] [--svg] [--size SIZE] [-s STRIP] [-c CAREFUL]
                seqs_of_interest assembly_dir

SeqFindr v 0.35.0 - A tool to easily create informative genomic feature plots

positional arguments:
  seqs_of_interest      Full path to FASTA file containing a set of sequences
                        of interest
  assembly_dir          Full path to directory containing a set of assemblies
                        in FASTA format

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         verbose output

Optional algorithm options:
  Options relating to the SeqFindr algorithm

  -t TOL, --tol TOL     Similarity cutoff [default = 0.95]
  -m CONS, --cons CONS  Full path to directory containing mapping consensuses
                        [default = None]. See manual for more info
  -r, --reshape         Differentiate between mapping and assembly hits in the
                        figure [default = no differentiation]
  --index_file INDEX_FILE
                        Maintain the y axis strain order according to order
                        given in this file. Otherwise clustering by row
                        similarity. [default = do clustering]. See manual for
                        more info
  -s STRIP, --strip STRIP
                        Strip the 1st and last N bases of mapping consensuses
                        & database [default = 10]
  -c CAREFUL, --careful CAREFUL
                        Manually consider hits that fall (tol-careful) below
                        the cutoff. [default = 0]. With default tol (0.95) &
                        careful = 0.2, we will manually inspect all hits in
                        0.95-0.75 range

Optional input/output options:
  Options relating to input and output

  -o OUTPUT, --output OUTPUT
                        Output the results to this location
  -p OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Give all result files this prefix
  --EXISTING_MATRIX     Use existing SeqFindr matrix (reformat the plot)
                        [default = False]

Figure options:
  Options relating to the output figure

  -l, --label_genes     Label the x axis with the query identifier [default =
  -g, --grid            Figure has grid lines [default = True]
  --color COLOR         The color index [default = None]. See manual for more
  --DPI DPI             DPI of figure [default = 300]
  --seed SEED           Color generation seed
  --svg                 Draws figure in svg
  --size SIZE           Size of figure [default = 10x12 (inches)]

BLAST options:
  Options relating to BLAST

  -R {nucl,prot}, --reftype {nucl,prot}
                        Reference Sequence type. If not given will try to
                        detect it
  -X, --tblastx         Run tBLASTx rather than BLASTn
  --evalue EVALUE       BLAST evalue (Expect)
  --short               Have short queries i.e. PCR Primers
                        Use this number of threads in BLAST run [default = 1]

Licence: ECL 2.0 by Mitchell Stanton-Cook, Nabil Alikhan & Hamza Khan


Something like this:

$ vfdb_to_seqfindr -h

usage: vfdb_to_seqfindr [-h] [-i INFILE] [-o OUTFILE] [-c CLASS_FILE] [-b]

Convert VFDB formatted files (or like) to SeqFindr formatted database files

optional arguments:
  -h, --help            show this help message and exit
  -i INFILE, --infile INFILE
                        [Required] fullpath to the in fasta file
  -o OUTFILE, --outfile OUTFILE
                        [Required] fullpath to the out fasta file
  -c CLASS_FILE, --class_file CLASS_FILE
                        [Optional] full path to a file containing factor
  -b, --blank_class     [Optional] set classification blank even if such exist

Licence: ECL by Mitchell Stanton-Cook <>