[re/factor] readme and changes

README.md

@@ -0,0 +1,56 @@
+# 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
+```

orffinder/orffinder.py

@@ -149,8 +149,8 @@ def getORFNucleotides (sequence, return_loci=False, **kwargs):
     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.
-    minimum_length: minimum size of ORF in nucleotides.
+    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
@@ -191,8 +191,9 @@ def getORFProteins (sequence, translation_table=1, return_loci=False, **kwargs):
     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 protein sequences.
-    minimum_length: minimum size of ORF in nucleotides.
+    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