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Predict ancestral sequence of fungal repeat elements by correcting for RIP-like mutations in multi-sequence DNA alignments.

Project description

# deRIP2

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

# Table of contents

* [Algorithm overview](#algorithm-overview)
* [Options and usage](#options-and-usage)
* [Installing deRIP2](#installing-derip2)
* [Example usage](#example-usage)
* [Standard options](#standard-options)
* [License](#license)

# Algorithm overview
# Options and usage

## Installing deRIP2

Clone from this repository:

```bash
git clone https://github.com/Adamtaranto/deRIP2.git && cd deRIP2
```
## Example usage

For aligned sequences in 'myalignment.fa':
- Any column >= 50% non RIP/cytosine deamination mutations is not corrected.
- Any column >= 70% gap positions is not corrected.
- Make RIP corrections if column is >= 10% RIP context.
- Correct Cytosine-deamination mutations outside of RIP context.
- Inherit all remaining uncorrected positions from least RIP'd sequence.

```bash
./deRIP2.py --inAln myalignment.fa --format fasta \
--maxGaps 0.7 \
--maxSNPnoise 0.5 \
--minRIPlike 0.1 \
--outName deRIPed_sequence.fa \
--outAlnName aligment_with_deRIP.aln \
--outAlnFormat clustal \
--label deRIPseqName \
--outDir results \
--reaminate
```

**Output:**
- results/aligment_with_deRIP.aln

## Standard options

```
Usage: ./deRIP2.py [-h] -i INALN
[--format {clustal,emboss,fasta,fasta-m10,ig,nexus,phylip,phylip-sequential,phylip-relaxed,stockholm}]
[--outAlnFormat {clustal,emboss,fasta,fasta-m10,ig,nexus,phylip,phylip-sequential,phylip-relaxed,stockholm}]
[-g MAXGAPS] [-a] [--maxSNPnoise MAXSNPNOISE]
[--minRIPlike MINRIPLIKE] [-o OUTNAME] [--outAlnName OUTALNNAME]
[--label LABEL] [-d OUTDIR]

Takes a multi-sequence DNA alignment and estimates a progenitor sequence by
correcting for RIP-like mutations.

Optional arguments:

# Info:

-h, --help Show this help message and exit.

# Input:

-i, --inAln Multiple sequence alignment.
(Required)
--format Format of the input alignment.
Accepted formats:
{clustal,emboss,fasta,fasta-m10,ig,nexus,phylip,phylip-sequential,phylip-relaxed,stockholm}

# Output:

--label Use label as name for deRIP'd sequence in output files.
-o, --outName Write deRIP sequence to this file.
-d, --outDir Directory for deRIP'd sequence files to be written to.
--outAlnName If set writes alignment including deRIP sequence to this file.
--outAlnFormat Write alignment including deRIP sequence to file of format X.
Accepted formats:
{clustal,emboss,fasta,fasta-m10,ig,nexus,phylip,phylip-sequential,phylip-relaxed,stockholm}

# deRIP settings:

-g, --maxGaps The maximum proportion of gapped positions in a column to be
tolerated before forcing a gap in the final deRIP sequence.
-a, --reaminate Correct deamination events in non-RIP contexts.
--maxSNPnoise The maximum proportion of conflicting SNPs permitted before
excluding a column from RIP/deamination assessment.
i.e. By default a column with >= 50 'C/T' bases will have
'TpA' positions logged as RIP events.
--minRIPlike 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.
```

# License

Software provided under MIT license.

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