changeset 26:52e50de4c005 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/local_AAComposition.py	Sun Dec 12 10:49:43 2021 +0000
@@ -0,0 +1,78 @@
+
+# -*- coding: utf-8 -*-
+"""
+The module is used for computing the composition of amino acids, dipetide and
+3-mers (tri-peptide) for a given protein sequence.
+References
+----------
+.. [1] Reczko, M. and Bohr, H. (1994) The DEF data base of sequence based protein
+   fold class predictions. Nucleic Acids Res, 22, 3616-3619.
+.. [2] Hua, S. and Sun, Z. (2001) Support vector machine approach for protein
+   subcellular localization prediction. Bioinformatics, 17, 721-728.
+.. [3] Grassmann, J., Reczko, M., Suhai, S. and Edler, L. (1999) Protein fold
+   class prediction: new methods of statistical classification. Proc Int Conf
+   Intell Syst Mol Biol, 106-112.
+Authors: Dongsheng Cao and Yizeng Liang.
+Date: 2012.3.27
+Email: [e-mail]
+"""
+
+# Core Library
+import re
+from typing import Any, Dict, List
+
+AALetter: List[str] = list("ARNDCEQGHILKMFPSTWYV")
+
+ProteinSequence_docstring = """ProteinSequence: str
+        a pure protein sequence"""
+
+
+def CalculateAAComposition(ProteinSequence: str) -> Dict[str, float]:
+    sequence_length = len(ProteinSequence)
+    result: Dict[str, float] = {}
+    for i in AALetter:
+        result[i] = round(float(ProteinSequence.count(i)) / sequence_length * 100, 3)
+    return result
+
+
+def CalculateDipeptideComposition(ProteinSequence: str) -> Dict[str, float]:
+    sequence_length = len(ProteinSequence)
+    result = {}
+    for i in AALetter:
+        for j in AALetter:
+            dipeptide = i + j
+            result[dipeptide] = round(
+                float(ProteinSequence.count(dipeptide)) / (sequence_length - 1) * 100, 2
+            )
+    return result
+
+
+def Getkmers() -> List[str]:
+    kmers = []
+    for i in AALetter:
+        for j in AALetter:
+            for k in AALetter:
+                kmers.append(i + j + k)
+    return kmers
+
+
+def GetSpectrumDict(proteinsequence: str) -> Dict[str, int]:
+    result = {}
+    kmers = Getkmers()
+    for i in kmers:
+        result[i] = len(re.findall(i, proteinsequence))
+    return result
+
+
+def CalculateAADipeptideComposition(ProteinSequence: str) -> Dict[str, float]:
+    result: Dict[Any, Any] = {}
+    result.update(CalculateAAComposition(ProteinSequence))
+    result.update(CalculateDipeptideComposition(ProteinSequence))
+    result.update(GetSpectrumDict(ProteinSequence))
+    return result
+
+
+
+
+
+