deRIP2

Predict progenitor sequence of fungal repeat families by correcting for RIP-like mutations (CpA --> TpA) and cytosine deamination (C --> T) events.

Mask RIP or deamination events from input alignment as ambiguous bases.

Table of contents

• Algorithm overview
• Options and Usage
  • Installation
  • Example usage
  • Standard options
• Report Issues
• License

Algorithm overview

For each column in input alignment:

• Check if number of gapped rows is greater than max gap proportion. If true, then a gap is added to the output sequence.
• Set invariant column values in output sequence.
• If at least X proportion of bases are C/T or G/A (i.e. maxSNPnoise = 0.4, then at least 0.6 of positions in column must be C/T or G/A).
• If reaminate option is set then revert T-->C or A-->G.
• If reaminate is not set then check for number of positions in RIP dinucleotide context (C/TpA or TpG/A).
• If proportion of positions in column in RIP-like context => minRIPlike threshold, AND at least one substrate and one product motif (i.e. CpA and TpA) is present, perform RIP correction in output sequence.
• For all remaining positions in output sequence (not filled by gap, reaminate, or RIP-correction) inherit sequence from input sequence with the fewest observed RIP events (or greatest GC content if not RIP detected or multiple sequences sharing min-RIP count).

Outputs:

• Corrected sequence as fasta.
• Optional, alignment with:
  • Corrected sequence appended.
  • With corrected positions masked as ambiguous bases.

Options and Usage

Installation

Requires Python => v3.8

Clone from this repository:

% git clone https://github.com/Adamtaranto/deRIP2.git && cd deRIP2 && pip install -e .

Install from PyPi.

% pip install derip2

Test installation.

# Print version number and exit.
% derip2 --version

derip2 0.0.4


# Get usage information
% derip2 --help

Example 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)

derip2 -i tests/data/mintest.fa --format fasta \
--maxGaps 0.7 \
--maxSNPnoise 0.2 \
--minRIPlike 0.5 \
--label derip_name \
--mask \
-d results \
--outAln masked_aligment_with_deRIP.fa --outAlnFormat fasta --outFasta derip_prediction.fa

Output:

• results/derip_prediction.fa
• results/masked_aligment_with_deRIP.fa

Issues

Submit feedback to the Issue Tracker

License

Software provided under MIT license.