DeRIP2 Command Line Interface

Basic usage

For aligned sequences in 'mintest.fa':

• Any column with >= 70% gap positions will not be corrected and a gap inserted in corrected sequence.
• Bases in column must be >= 80% C/T or G/A
• At least 50% bases in a column must be in RIP dinucleotide context (C/T as CpA / TpA) for correction.
• Default: Inherit all remaining uncorrected positions from the least RIP'd sequence.
• Mask all substrate and product motifs from corrected columns as ambiguous bases (i.e. CpA to TpA --> YpA)

Basic usage with masking

derip2 -i tests/data/mintest.fa \
  --max-gaps 0.7 \
  --max-snp-noise 0.2 \
  --min-rip-like 0.5 \
  --mask \
  -d results \
  --prefix derip_output

Output:

• results/derip_output.fasta - Corrected sequence
• results/derip_output_alignment.fasta - Alignment with masked corrections
• results/derip_output_masked_alignment.fasta - Alignment with masked corrections

With vizualization

The --plot option will create a visualization of the alignment with RIP markup. The --plot-rip-type option can be used to specify the type of RIP events to be displayed in the alignment visualization product, substrate, or both.

derip2 -i tests/data/mintest.fa \
  --max-gaps 0.7 \
  --max-snp-noise 0.2 \
  --min-rip-like 0.5 \
  --plot \
  --plot-rip-type both \
  -d results \
  --prefix derip_output

Output:

• results/derip_output.fasta - Corrected sequence
• results/derip_output_masked_alignment.fasta - Alignment with masked corrections
• results/derip_output_visualization.png - Visualization of the alignment with RIP markup

Using maximum GC content for filling

By default uncorrected positions in the output sequence are filled from the sequence with the lowest RIP count. If the --fill-max-gc option is set, remaining positions are filled from the sequence with the highest G/C content sequence instead.

derip2 -i tests/data/mintest.fa \
  --max-gaps 0.7 \
  --max-snp-noise 0.2 \
  --min-rip-like 0.5 \
  --fill-max-gc \
  -d results \
  --prefix derip_gc_filled

Alternatively, the --fill-index option can be used to force selection of alignment row to fill uncorrected positions from by row index number (indexed from 0). Note: This will override the --fill-max-gc option.

Correcting all deamination events

If the --reaminate option is set, all deamination events will be corrected, regardless of RIP context.

--plot-rip-type product is used to highlight the product of RIP events in the visualization. Non-RIP deamination events are also highlighted.

derip2 -i tests/data/mintest.fa \
  --max-gaps 0.7 \
  --reaminate \
  -d results \
  --plot \
  --plot-rip-type product \
  --prefix derip_reaminated

Output:

• results/derip_reaminated.fasta - Corrected sequence using highest GC content sequence for filling
• results/derip_reaminated_alignment.fasta - Alignment with corrected sequence appended
• results/derip_reaminated_vizualization.png - Visualization of the alignment with RIP markup

Standard Options

  --version                       Show the version and exit.
  -i, --input TEXT                Multiple sequence alignment.  [required]
  -g, --max-gaps FLOAT            Maximum proportion of gapped positions in
                                  column to be tolerated before forcing a gap
                                  in final deRIP sequence.  [default: 0.7]
  -a, --reaminate                 Correct all deamination events independent
                                  of RIP context.
  --max-snp-noise FLOAT           Maximum proportion of conflicting SNPs
                                  permitted before excluding column from
                                  RIP/deamination assessment. i.e. By default
                                  a column with >= 0.5 'C/T' bases will have
                                  'TpA' positions logged as RIP events.
                                  [default: 0.5]
  --min-rip-like FLOAT            Minimum proportion of deamination events in
                                  RIP context (5' CpA 3' --> 5' TpA 3')
                                  required for column to deRIP'd in final
                                  sequence. Note: If 'reaminate' option is set
                                  all deamination events will be corrected.
                                  [default: 0.1]
  --fill-max-gc                   By default uncorrected positions in the
                                  output sequence are filled from the sequence
                                  with the lowest RIP count. If this option is
                                  set remaining positions are filled from the
                                  sequence with the highest G/C content.
  --fill-index INTEGER            Force selection of alignment row to fill
                                  uncorrected positions from by row index
                                  number (indexed from 0). Note: Will override
                                  '--fill-max-gc' option.
  --mask                          Mask corrected positions in alignment with
                                  degenerate IUPAC codes.
  --no-append                     If set, do not append deRIP'd sequence to
                                  output alignment.
  -d, --out-dir TEXT              Directory for deRIP'd sequence files to be
                                  written to.
  -p, --prefix TEXT               Prefix for output files. Output files will
                                  be named prefix.fasta,
                                  prefix_alignment.fasta, etc.  [default:
                                  deRIPseq]
  --plot                          Create a visualization of the alignment with
                                  RIP markup.
  --plot-rip-type [both|product|substrate]
                                  Specify the type of RIP events to be
                                  displayed in the alignment visualization.
                                  [default: both]
  --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]
                                  Set logging level.  [default: INFO]
  --logfile TEXT                  Log file path.
  -h, --help                      Show this message and exit.