Created
September 28, 2011 12:18
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Python Scripting for Williams Bio319
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| #!/usr/bin/env python3 | |
| # cc attribution-sharealike // max [@] maxnanis.com | |
| import re | |
| from bio import fastad, fastac, rc | |
| # set up a standard code table (as a Python dictionary) | |
| # takes in a nucleotide string and returns the amino acid string | |
| stdcode = {} | |
| stdcode["TTT"] = stdcode["TTC"] = "F" | |
| stdcode["TTA"] = stdcode["TTG"] = "L" | |
| stdcode["TCT"] = stdcode["TCC"] = stdcode["TCA"] = stdcode["TCG"] = "S" | |
| stdcode["TAT"] = stdcode["TAC"] = "Y" | |
| stdcode["TAA"] = stdcode["TAG"] = "*" #stop codon | |
| stdcode["TGT"] = stdcode["TGC"] = "C" | |
| stdcode["TGA"] = "*" #stop codon | |
| stdcode["TGG"] = "W" | |
| stdcode["CTT"] = stdcode["CTC"] = stdcode["CTA"] = stdcode["CTG"] = "L" | |
| stdcode["CCT"] = stdcode["CCC"] = stdcode["CCA"] = stdcode["CCG"] = "P" | |
| stdcode["CAT"] = stdcode["CAC"] = "H" | |
| stdcode["CAA"] = stdcode["CAG"] = "Q" | |
| stdcode["CGT"] = stdcode["CGC"] = stdcode["CGA"] = stdcode["CGG"] = "R" | |
| stdcode["ATT"] = stdcode["ATC"] = stdcode["ATA"] = "I" | |
| stdcode["ATG"] = "M" | |
| stdcode["ACT"] = stdcode["ACC"] = stdcode["ACA"] = stdcode["ACG"] = "T" | |
| stdcode["AAT"] = stdcode["AAC"] = "N" | |
| stdcode["AAA"] = stdcode["AAG"] = "K" | |
| stdcode["AGT"] = stdcode["AGC"] = "S" | |
| stdcode["AGA"] = stdcode["AGG"] = "R" | |
| stdcode["GTT"] = stdcode["GTC"] = stdcode["GTA"] = stdcode["GTG"] = "V" | |
| stdcode["GCT"] = stdcode["GCC"] = stdcode["GCA"] = stdcode["GCG"] = "A" | |
| stdcode["GAT"] = stdcode["GAC"] = "D" | |
| stdcode["GAA"] = stdcode["GAG"] = "E" | |
| stdcode["GGT"] = stdcode["GGC"] = stdcode["GGA"] = stdcode["GGG"] = "G" | |
| def translate(nt_list, frame = 0, code = stdcode): | |
| results = [] | |
| # loop through nt lists and store its amino acid | |
| for nt in nt_list: | |
| # pos starts at i+frameoffset defined by user and will increase as we go through each nt | |
| pos = 0+frame | |
| # indent nicely (currently: none) | |
| aa = ' '*pos | |
| # get the next three letters from the nt | |
| codon = nt[pos:pos+3] | |
| # as long as we have a complete codon, when offset - the last will cut off 1-2 bases short | |
| while len(codon) == 3: | |
| # handled by mapping? | |
| cdn = code[codon] | |
| if cdn: | |
| # yes: include aa code | |
| aa += cdn + " " | |
| else: | |
| # no: include an * | |
| aa = aa + "*" | |
| # march along, 3nt | |
| pos += 3 | |
| codon = nt[pos:pos+3] | |
| # append the translation to the results | |
| results.append(aa) | |
| return results | |
| def render(nt, frame): | |
| # if frame is >= 3, perhaps that means to work on reverse complement | |
| rvs = "Nah" | |
| if frame >= 3: | |
| rvs = "Yup" | |
| nt = rc(nt) | |
| frame = frame - 3 | |
| print("\n Reading frame {}, Reversed: ".format(frame)+rvs+"\n\n") | |
| aa = translate(nt, frame) | |
| for i in range(len(nt)): | |
| print(nt[i]) | |
| print(aa[i]) | |
| if __name__ == "__main__": | |
| # argv a list of words in command; eg. argv[0] is usually 'translate' | |
| from sys import stdin, argv | |
| nt = fastad(stdin.readlines()) | |
| if len(argv) == 1: | |
| # if no arguments were passed in | |
| # do all possible frames/reverses | |
| for frame in range(0,6): | |
| render(nt, frame) | |
| else: | |
| # if frame argument was passed in | |
| render(nt, int(argv[1])) |
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