Metadata-Version: 1.2
Name: derip2
Version: 0.0.1
Summary: Predict ancestral sequence of fungal repeat elements by correcting for RIP-like mutations in multi-sequence DNA alignments.
Home-page: https://github.com/Adamtaranto/deRIP2
Author: Adam Taranto
Author-email: adam.taranto@anu.edu.au
License: MIT
Description-Content-Type: UNKNOWN
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.
Keywords: Transposon,RIP,TE
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >= 3.6
