Metadata-Version: 2.1
Name: orffinder
Version: 1.0.0
Summary: ORFFinder API.
Home-page: https://github.com/Chokyotager/ORFFinder
Author: ChocoParrot
Author-email: lachocoparrot@gmail.com
License: UNKNOWN
Description: # ORFFinder
        ORFFinder in Python. Inspired by NCBI's version: https://www.ncbi.nlm.nih.gov/orffinder/
        
        ### Installation:
        `pip3 install orffinder`
        
        ### Usage
        Import the package
        
        ```py
        from Bio import SeqIO
        import orffinder
        
        sequence = SeqIO.read("gene.fasta", "fasta")
        orffinder.getORFs(sequence, minimum_length=75, remove_nested=True)
        ```
        
        ### Documentation
        **getORFs()**
        ```
        Returns the loci of discovered ORFs in a dictionary format.
        
        sequence: sequence in Biopython Seq or String format.
        minimum_length: minimum size of ORF in nucleotides. Default: 75
        start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"]
        stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"]
        remove_nested: remove all ORFs completely encased in another. Default: False
        trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False
        ```
        
        **getORFNucleotides()**
        ```
        Returns the loci of discovered ORFs in a dictionary format.
        
        sequence: sequence in Biopython Seq or String format.
        return_loci: return the loci together with the nucleotide sequences. Default: False
        minimum_length: minimum size of ORF in nucleotides. Default: 75
        start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"]
        stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"]
        remove_nested: remove all ORFs completely encased in another. Default: False
        trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False
        ```
        
        **getORFProteins()**
        ```
        Returns the loci of discovered ORFs in a dictionary format.
        
        sequence: sequence in Biopython Seq or String format.
        translation_table: translation table as per BioPython. Default: 1
        return_loci: return the loci together with the protein sequences. Default: False
        minimum_length: minimum size of ORF in nucleotides. Default: 75
        start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"]
        stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"]
        remove_nested: remove all ORFs completely encased in another. Default: False
        trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
