changeset 2:c56b8a6bd02e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GTranslator.py	Wed Oct 12 00:03:46 2016 -0400
@@ -0,0 +1,196 @@
+"""
+ Translate nucleotide code to polypeptide
+ Because condon table is never change, so in consider of read/exe performance,
+ it is hard-coded, not writen in XML or other format of files, nor store in database
+ TODO: Need to add condon table for RNA
+
+ Author Nedias
+"""
+
+from Bio.Alphabet import generic_protein
+from Bio.Seq import Seq
+
+
+# Nucleotide to Polypeptide mapping
+def condon_table():
+    c_table = dict()
+
+    c_table["TTT"] = "F"
+    c_table["TTC"] = "F"
+    c_table["TTA"] = "L"
+    c_table["TTG"] = "L"
+    c_table["CTT"] = "L"
+    c_table["CTC"] = "L"
+    c_table["CTA"] = "L"
+    c_table["CTG"] = "L"
+    c_table["ATT"] = "I"
+    c_table["ATC"] = "I"
+    c_table["ATA"] = "I"
+    c_table["ATG"] = "M"
+    c_table["GTT"] = "V"
+    c_table["GTC"] = "V"
+    c_table["GTA"] = "V"
+    c_table["GTG"] = "V"
+    c_table["TCT"] = "S"
+    c_table["TCA"] = "S"
+    c_table["TCC"] = "S"
+    c_table["TCG"] = "S"
+    c_table["CCT"] = "P"
+    c_table["CCC"] = "P"
+    c_table["CCA"] = "P"
+    c_table["CCG"] = "P"
+    c_table["ACT"] = "T"
+    c_table["ACC"] = "T"
+    c_table["ACA"] = "T"
+    c_table["ACG"] = "T"
+    c_table["GCT"] = "A"
+    c_table["GCC"] = "A"
+    c_table["GCA"] = "A"
+    c_table["GCG"] = "A"
+    c_table["TAT"] = "Y"
+    c_table["TAC"] = "Y"
+    c_table["TAA"] = "stop"
+    c_table["TAG"] = "stop"
+    c_table["CAT"] = "H"
+    c_table["CAC"] = "H"
+    c_table["CAA"] = "Q"
+    c_table["CAG"] = "Q"
+    c_table["AAT"] = "N"
+    c_table["AAC"] = "N"
+    c_table["AAA"] = "K"
+    c_table["AAG"] = "K"
+    c_table["GAT"] = "D"
+    c_table["GAC"] = "D"
+    c_table["GAA"] = "E"
+    c_table["GAG"] = "E"
+    c_table["TGT"] = "C"
+    c_table["TGC"] = "C"
+    c_table["TGA"] = "stop"
+    c_table["TGG"] = "W"
+    c_table["CGT"] = "R"
+    c_table["CGC"] = "R"
+    c_table["CGA"] = "R"
+    c_table["CGG"] = "R"
+    c_table["AGT"] = "S"
+    c_table["AGC"] = "S"
+    c_table["AGA"] = "R"
+    c_table["AGG"] = "R"
+    c_table["GGT"] = "G"
+    c_table["GGC"] = "G"
+    c_table["GGA"] = "G"
+    c_table["GGG"] = "G"
+    c_table.update(dict((c_table[i], i) for i in c_table))
+
+    return c_table
+
+
+# Nucleotide to Polypeptide mapping for complementary sequence
+def rev_condon_table():
+
+    c_table = dict()
+
+    c_table["AAA"] = "F"
+    c_table["AAG"] = "F"
+    c_table["AAT"] = "L"
+    c_table["AAC"] = "L"
+    c_table["GAA"] = "L"
+    c_table["GAG"] = "L"
+    c_table["GAT"] = "L"
+    c_table["GAC"] = "L"
+    c_table["TAA"] = "I"
+    c_table["TAG"] = "I"
+    c_table["TAT"] = "I"
+    c_table["TAC"] = "M"
+    c_table["CAA"] = "V"
+    c_table["CAG"] = "V"
+    c_table["CAT"] = "V"
+    c_table["CAC"] = "V"
+    c_table["AGA"] = "S"
+    c_table["AGT"] = "S"
+    c_table["AGG"] = "S"
+    c_table["AGC"] = "S"
+    c_table["GGA"] = "P"
+    c_table["GGG"] = "P"
+    c_table["GGT"] = "P"
+    c_table["GGC"] = "P"
+    c_table["TGA"] = "T"
+    c_table["TGG"] = "T"
+    c_table["TGT"] = "T"
+    c_table["TGC"] = "T"
+    c_table["CGA"] = "A"
+    c_table["CGG"] = "A"
+    c_table["CGT"] = "A"
+    c_table["CGC"] = "A"
+    c_table["ATA"] = "Y"
+    c_table["ATG"] = "Y"
+    c_table["ATT"] = "stop"
+    c_table["ATC"] = "stop"
+    c_table["GTA"] = "H"
+    c_table["GTG"] = "H"
+    c_table["GTT"] = "Q"
+    c_table["GTC"] = "Q"
+    c_table["TTA"] = "N"
+    c_table["TTG"] = "N"
+    c_table["TTT"] = "K"
+    c_table["TTC"] = "K"
+    c_table["CTA"] = "D"
+    c_table["CTG"] = "D"
+    c_table["CTT"] = "E"
+    c_table["CTC"] = "E"
+    c_table["ACA"] = "C"
+    c_table["ACG"] = "C"
+    c_table["ACT"] = "stop"
+    c_table["ACC"] = "W"
+    c_table["GCA"] = "R"
+    c_table["GCG"] = "R"
+    c_table["GCT"] = "R"
+    c_table["GCC"] = "R"
+    c_table["TCA"] = "S"
+    c_table["TCG"] = "S"
+    c_table["TCT"] = "R"
+    c_table["TCC"] = "R"
+    c_table["CCA"] = "G"
+    c_table["CCG"] = "G"
+    c_table["CCT"] = "G"
+    c_table["CCC"] = "G"
+    c_table.update(dict((c_table[i], i) for i in c_table))
+
+    return c_table
+
+
+# Check if the sequence is a multiple of 3
+# input: Nucleotide sequence in SeqRecords format or string format
+# output: check result
+def check_seq(seq):
+
+    if len(seq) % 3 == 0:
+        return True
+    else:
+        return False
+
+
+# Translate Nucleotide to Polypeptide
+# input: 1.seq: Nucleotide sequence in SeqRecords format
+#        2.rev: True if +strand(use normal mapping), False for -strand(use complementary mapping)
+# return: Polypeptide sequence in Seq format
+def nucleotide_to_polypeptide(seq, rev):
+
+    poly_seq = ""
+    # If -strand, use complementary mapping
+    if rev:
+        c_table = rev_condon_table()
+    # If +strand, use normal mapping
+    else:
+        c_table = condon_table()
+
+    # If sequence length is a multiple of 3
+    if check_seq(seq):
+        str_seq = str(seq)
+        # Translate every 3 nucleotide acid to one polypeptide
+        for i in xrange(0, len(str_seq) - 3, 3):
+            poly_seq += c_table[str_seq[i:i+3]]
+    return Seq(poly_seq, generic_protein)
+
+
+
+