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397 lines
17 KiB
Python
397 lines
17 KiB
Python
#!/usr/bin/env python3.5
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##__Updated__: 19_09_2017
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##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
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##__Usage__: python 3g_GCodeTranslate.py --help
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##############################################################################
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## ##
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## Translates CDSs sequences using the Provided Genetic Code. ##
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## ##
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## NOTE: ##
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## No provided input for genetic code results in Translation with the ##
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## UNIVERSAL genetic code (as default) ##
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## ##
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## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
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## ##
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##############################################################################
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import argparse, os, sys
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from argparse import RawTextHelpFormatter,SUPPRESS
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from Bio import SeqIO
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from Bio.Seq import Seq
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from Bio.Data.CodonTable import CodonTable
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#-------------------------- Set-up Codon Tables (Genetic Codes) --------------------------#
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blepharisma_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y',
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'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = ['TAA','TAG'])
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condylostoma_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q', 'TAG': 'Q',
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'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = [''])
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c_uncinata_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y', 'TAG': 'Q',
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'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = ['TAA'])
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euplotes_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y',
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'TGT': 'C', 'TGC': 'C', 'TGA': 'C', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = ['TAA','TAG'])
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myrionecta_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Y', 'TAG': 'Y',
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'TGT': 'C', 'TGC': 'C', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = ['TGA'])
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no_stop_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y', 'TAA': 'X', 'TAG': 'X',
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'TGT': 'C', 'TGC': 'C', 'TGA': 'X', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = [''])
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peritrich_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y', 'TAA': 'E', 'TAG': 'E',
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'TGT': 'C', 'TGC': 'C', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = ['TGA'])
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tag_table = CodonTable(forward_table={
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q',
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'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W',
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'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L',
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'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
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'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q',
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'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
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'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M',
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'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
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'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K',
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'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
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'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V',
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'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
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'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E',
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'},
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start_codons = [ 'ATG'],
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stop_codons = ['TAG'])
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#----------------------------- Colors For Print Statements ------------------------------#
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class color:
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PURPLE = '\033[95m'
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CYAN = '\033[96m'
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DARKCYAN = '\033[36m'
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ORANGE = '\033[38;5;214m'
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BLUE = '\033[94m'
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GREEN = '\033[92m'
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YELLOW = '\033[93m'
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RED = '\033[91m'
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BOLD = '\033[1m'
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UNDERLINE = '\033[4m'
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END = '\033[0m'
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#------------------------------- Main Functions of Script --------------------------------#
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###########################################################################################
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###------------------------- Checks the Command Line Arguments -------------------------###
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###########################################################################################
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def check_args():
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parser = argparse.ArgumentParser(description=
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color.BOLD + '\n\nThis script will '+color.RED+'Translate '+color.END+color.BOLD+'a '\
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'given Fasta file of CDS\nsequences using a given'+color.PURPLE+' Genetic Code.'+color.END+\
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color.BOLD+usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter)
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required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END)
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required_arg_group.add_argument('--input_file','-in', action='store',
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help=color.BOLD+color.GREEN+' Fasta file with CDSs\n'+color.END)
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optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
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optional_arg_group.add_argument('--genetic_code','-g', action='store', default='universal',
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help=color.BOLD+color.GREEN+' Genetic code to use for translation\n (default = '\
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'"universal")\n'+color.END)
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optional_arg_group.add_argument('--list_codes','-codes', action='store_true',
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help=color.BOLD+color.GREEN+' Lists supported genetic codes\n'+color.END)
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optional_arg_group.add_argument('-author', action='store_true',
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help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END)
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if len(sys.argv[1:]) == 0:
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print (parser.description)
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print ('\n')
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sys.exit()
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args = parser.parse_args()
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quit_eval = return_more_info(args)
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if quit_eval > 0:
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sys.exit()
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args.folder = '../'+args.input_file.split('/')[1]
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args.out_name = args.input_file.split('.Prepped')[0]+'.'+args.genetic_code.title()+'.AA.fasta'
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args.new_ntd_name = args.input_file.split('.Prepped')[0]+'.'+args.genetic_code.title()+'.NTD.fasta'
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return args
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###########################################################################################
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###------------------------------- Script Usage Message --------------------------------###
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###########################################################################################
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def usage_msg():
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return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 3g_GCodeTranslate.py'\
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' --input_file ../Stentor_coeruleus.WGS.CDS.Prep/Stentor_coeruleus.WGS.CDS.Prepped.fasta'\
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' --genetic_code Universal'+color.END)
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##########################################################################################
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###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------###
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##########################################################################################
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def return_more_info(args):
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valid_arg = 0
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supported_gcodes_names = ['bleph','blepharisma','chilo','chilodonella','condy',\
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'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal',\
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'taa','tag','tga']
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supported_gcodes_list = ['Blepharisma\t(TGA = W)','Chilodonella\t(TAG/TGA = Q)','Ciliate\t\t(TAR = Q)',\
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'Conylostoma\t(TAR = Q, TGA = W)','Euplotes\t(TGA = C)','Peritrich\t(TAR = E)','None\t\t(TGA/TAG/TAA = X)',\
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'Universal\t(TGA/TAG/TAA = STOP)','TAA\t\t(TAG/TGA = Q)', 'TAG\t\t(TRA = Q)', 'TGA\t\t(TAR = Q)']
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author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\
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' maurerax@gmail.com\n\n'+color.END)
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if args.genetic_code != None and args.genetic_code.lower() not in supported_gcodes_names:
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print (color.BOLD+color.RED+'\nProvided genetic code is currently unsupported.\n\n'\
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'If you have a new genetic code, please contact the author (with some evidence).\n\n'\
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'Otherwise, use one of the currently supported genetic codes.\n'+color.END)
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print (color.BOLD+color.ORANGE+'\n'.join(supported_gcodes_list)+'\n\n'+color.END)
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print (author)
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valid_arg += 1
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else:
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if args.list_codes == True:
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print (color.BOLD+color.RED+'\nThese are the currently supported genetic codes.\n'+color.END)
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print (color.BOLD+color.ORANGE+'\n'.join(supported_gcodes_list)+'\n\n'+color.END)
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valid_arg += 1
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if args.author == True:
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print (author)
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valid_arg += 1
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if args.input_file != None:
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if os.path.isfile(args.input_file) != False:
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if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])):
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
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'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
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' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
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valid_arg += 1
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else:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
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'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
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' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
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valid_arg += 1
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return valid_arg
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##########################################################################################
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###------------------ Translates CDSs from the Provided Genetic Code ------------------###
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##########################################################################################
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def translate_seqs(args):
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inFasta = [i for i in SeqIO.parse(args.input_file,'fasta')]
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print (color.BOLD+'\n\n\nTranslating: '+color.CYAN+args.input_file.split('/')[-1]+color.END+\
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color.BOLD+'\nwith the '+color.GREEN+args.genetic_code.upper()+' Genetic Code\n'+color.END)
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if args.genetic_code.lower() == 'ciliate' or args.genetic_code.lower() == 'tga':
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translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=6)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta]
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if args.genetic_code.lower() == 'peritrich' or args.genetic_code.lower() == 'vorticella':
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translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=peritrich_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta]
|
|
|
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if args.genetic_code.lower() == 'tag':
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translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=tag_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta]
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|
|
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if args.genetic_code.lower() == 'chilo' or args.genetic_code.lower() == 'chilodonella' or args.genetic_code.lower() == 'taa':
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translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=c_uncinata_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta]
|
|
|
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if args.genetic_code.lower() == 'bleph' or args.genetic_code.lower() == 'blepharisma':
|
|
translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=blepharisma_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta]
|
|
|
|
if args.genetic_code.lower() == 'eup' or args.genetic_code.lower() == 'euplotes':
|
|
translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=euplotes_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta]
|
|
|
|
if args.genetic_code.lower() == 'universal':
|
|
translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=1)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta]
|
|
|
|
return translated_seqs
|
|
|
|
|
|
##########################################################################################
|
|
###---------------------------- Writes Out Translated CDSs ----------------------------###
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|
##########################################################################################
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|
|
|
def write_out(args):
|
|
|
|
translated_seqs = translate_seqs(args)
|
|
|
|
## Keep only ORFs greater than 10 amino acids long
|
|
translated_seqs = [i for i in translated_seqs if len(i.split('\n')[1]) > 10]
|
|
|
|
print (color.BOLD+'\nTranslated '+color.ORANGE+str(len(translated_seqs))+color.END\
|
|
+color.BOLD+' seqeunces using the '+color.GREEN+args.genetic_code.upper()+' Genetic Code\n\n'+color.END)
|
|
|
|
with open(args.out_name,'w+') as w:
|
|
w.write(''.join(translated_seqs))
|
|
|
|
|
|
##########################################################################################
|
|
###--------------------- Cleans up the Folder and Moves Final Files -------------------###
|
|
##########################################################################################
|
|
|
|
def clean_up(args):
|
|
|
|
os.system('mv '+args.input_file+' '+args.new_ntd_name)
|
|
|
|
|
|
##########################################################################################
|
|
###----------------------------- Calls on Above Functions -----------------------------###
|
|
##########################################################################################
|
|
|
|
def main():
|
|
|
|
args = check_args()
|
|
|
|
write_out(args)
|
|
|
|
clean_up(args)
|
|
|
|
print (color.BOLD+'Next Script is: '+color.PURPLE+' 4g_CountOgsUsearch.py\n\n'+color.END)
|
|
|
|
main() |