SARS-Cov-2 Recombinant Finder for fasta sequences

sc2rf.py <your_filename.fasta>

sc2rf.py --parents 1-35 --breakpoints 0-100 \
--unique 1 --max-ambiguous 10000 <your_filename.fasta>

sc2rf.py --parents 1-35 --breakpoints 0-100 \
--unique 1 --max-ambiguous 10000 --force-all-parents \
--clades all <your_filename.fasta>

usage: sc2rf.py [-h] [--primers [PRIMER ...]]
                [--primer-intervals [INTERVAL ...]]
                [--parents INTERVAL] [--breakpoints INTERVAL]
                [--clades [CLADES ...]] [--unique NUM]
                [--max-intermission-length NUM]
                [--max-intermission-count NUM]
                [--max-name-length NUM] [--max-ambiguous NUM]
                [--force-all-parents]
                [--select-sequences INTERVAL]
                [--enable-deletions] [--show-private-mutations]
                [--rebuild-examples] [--mutation-threshold NUM]
                [--add-spaces [NUM]] [--sort-by-id [NUM]]
                [--verbose] [--ansi] [--hide-progress]
                [--csvfile CSVFILE]
                [input ...]

Analyse SARS-CoV-2 sequences for potential, unknown recombinant
variants.

positional arguments:
  input                 input sequence(s) to test, as aligned
                        .fasta file(s) (default: None)

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

  --primers [PRIMER ...]
                        Filenames of primer set(s) to visualize.
                        The .bed formats for ARTIC and EasySeq
                        are recognized and supported. (default:
                        None)

  --primer-intervals [INTERVAL ...]
                        Coordinate intervals in which to
                        visualize primers. (default: None)

  --parents INTERVAL, -p INTERVAL
                        Allowed number of potential parents of a
                        recombinant. (default: 2-4)

  --breakpoints INTERVAL, -b INTERVAL
                        Allowed number of breakpoints in a
                        recombinant. (default: 1-4)

  --clades [CLADES ...], -c [CLADES ...]
                        List of variants which are considered as
                        potential parents. Use Nextstrain clades
                        (like "21B"), or Pango Lineages (like
                        "B.1.617.1") or both. Also accepts "all".
                        (default: ['20I', '20H', '20J', '21I',
                        '21J', 'BA.1', 'BA.2', 'BA.3'])

  --unique NUM, -u NUM  Minimum of substitutions in a sample
                        which are unique to a potential parent
                        clade, so that the clade will be
                        considered. (default: 2)

  --max-intermission-length NUM, -l NUM
                        The maximum length of an intermission in
                        consecutive substitutions. Intermissions
                        are stretches to be ignored when counting
                        breakpoints. (default: 2)

  --max-intermission-count NUM, -i NUM
                        The maximum number of intermissions which
                        will be ignored. Surplus intermissions
                        count towards the number of breakpoints.
                        (default: 8)

  --max-name-length NUM, -n NUM
                        Only show up to NUM characters of sample
                        names. (default: 30)

  --max-ambiguous NUM, -a NUM
                        Maximum number of ambiguous nucs in a
                        sample before it gets ignored. (default:
                        50)

  --force-all-parents, -f
                        Force to consider all clades as potential
                        parents for all sequences. Only useful
                        for debugging.

  --select-sequences INTERVAL, -s INTERVAL
                        Use only a specific range of input
                        sequences. DOES NOT YET WORK WITH
                        MULTIPLE INPUT FILES. (default: 0-999999)

  --enable-deletions, -d
                        Include deletions in lineage comparision.

  --show-private-mutations
                        Display mutations which are not in any of
                        the potential parental clades.

  --rebuild-examples, -r
                        Rebuild the mutations in examples by
                        querying cov-spectrum.org.

  --mutation-threshold NUM, -t NUM
                        Consider mutations with a prevalence of
                        at least NUM as mandatory for a clade
                        (range 0.05 - 1.0, default: 0.75).

  --add-spaces [NUM]    Add spaces between every N colums, which
                        makes it easier to keep your eye at a
                        fixed place. (default without flag: 0,
                        default with flag: 5)

  --sort-by-id [NUM]    Sort the input sequences by the ID. If
                        you provide NUM, only the first NUM
                        characters are considered. Useful if this
                        correlates with meaning full meta
                        information, e.g. the sequencing lab.
                        (default without flag: 0, default with
                        flag: 999)

  --verbose, -v         Print some more information, mostly
                        useful for debugging.

  --ansi                Use only ASCII characters to be
                        compatible with ansilove.

  --hide-progress       Don't show progress bars during long
                        task.

  --csvfile CSVFILE     Path to write results in CSV format.
                        (default: None)

An Interval can be a single number ("3"), a closed interval
("2-5" ) or an open one ("4-" or "-7"). The limits are inclusive.
Only positive numbers are supported.