Mercurial > repos > nedias > orf_tools
view GTranslator.py @ 2:c56b8a6bd02e draft
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author | nedias |
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date | Wed, 12 Oct 2016 00:03:46 -0400 |
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""" 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)