Mercurial > repos > peterjc > align_back_trans
annotate tools/align_back_trans/align_back_trans.py @ 4:c8469274d136 draft
v0.0.8 Using Biopython 1.67 from Tool Shed or Conda package
| author | peterjc |
|---|---|
| date | Wed, 10 May 2017 12:05:28 -0400 |
| parents | de803005027f |
| children | 2c32e8a8990f |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 """Back-translate a protein alignment to nucleotides | |
| 3 | |
| 4 This tool is a short Python script (using Biopython library functions) to | |
| 5 load a protein alignment, and matching nucleotide FASTA file of unaligned | |
| 6 sequences, in order to produce a codon aware nucleotide alignment - which | |
| 7 can be viewed as a back translation. | |
| 8 | |
| 9 The development repository for this tool is here: | |
| 10 | |
| 3 | 11 * https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans |
| 0 | 12 |
| 13 This tool is available with a Galaxy wrapper from the Galaxy Tool Shed at: | |
| 14 | |
| 15 * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans | |
| 16 | |
| 17 See accompanying text file for licence details (MIT licence). | |
| 18 """ | |
| 19 | |
| 20 import sys | |
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21 |
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22 from Bio import AlignIO |
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23 from Bio import SeqIO |
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24 |
| 0 | 25 from Bio.Align import MultipleSeqAlignment |
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26 from Bio.Alphabet import generic_protein |
| 0 | 27 from Bio.Data.CodonTable import ambiguous_generic_by_id |
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28 from Bio.Seq import Seq |
| 0 | 29 |
| 30 if "-v" in sys.argv or "--version" in sys.argv: | |
| 3 | 31 print "v0.0.7" |
| 0 | 32 sys.exit(0) |
| 33 | |
| 34 | |
| 35 def check_trans(identifier, nuc, prot, table): | |
| 36 """Returns nucleotide sequence if works (can remove trailing stop)""" | |
| 37 if len(nuc) % 3: | |
| 3 | 38 sys.exit("Nucleotide sequence for %s is length %i (not a multiple of three)" |
| 1 | 39 % (identifier, len(nuc))) |
| 0 | 40 |
| 41 p = str(prot).upper().replace("*", "X") | |
| 42 t = str(nuc.translate(table)).upper().replace("*", "X") | |
| 43 if len(t) == len(p) + 1: | |
| 44 if str(nuc)[-3:].upper() in ambiguous_generic_by_id[table].stop_codons: | |
| 3 | 45 # Allow this... |
| 0 | 46 t = t[:-1] |
| 3 | 47 nuc = nuc[:-3] # edit return value |
| 0 | 48 if len(t) != len(p): |
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49 err = ("Inconsistent lengths for %s, ungapped protein %i, " |
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50 "tripled %i vs ungapped nucleotide %i." % |
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51 (identifier, len(p), len(p) * 3, len(nuc))) |
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52 if t.endswith(p): |
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53 err += "\nThere are %i extra nucleotides at the start." % (len(t) - len(p)) |
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54 elif t.startswith(p): |
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55 err += "\nThere are %i extra nucleotides at the end." % (len(t) - len(p)) |
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56 elif p in t: |
| 3 | 57 # TODO - Calculate and report the number to trim at start and end? |
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58 err += "\nHowever, protein sequence found within translated nucleotides." |
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59 elif p[1:] in t: |
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60 err += "\nHowever, ignoring first amino acid, protein sequence found within translated nucleotides." |
| 3 | 61 sys.exit(err) |
| 0 | 62 |
| 63 if t == p: | |
| 64 return nuc | |
| 65 elif p.startswith("M") and "M" + t[1:] == p: | |
| 3 | 66 # Close, was there a start codon? |
| 0 | 67 if str(nuc[0:3]).upper() in ambiguous_generic_by_id[table].start_codons: |
| 68 return nuc | |
| 69 else: | |
| 3 | 70 sys.exit("Translation check failed for %s\n" |
| 0 | 71 "Would match if %s was a start codon (check correct table used)\n" |
| 72 % (identifier, nuc[0:3].upper())) | |
| 73 else: | |
| 3 | 74 # Allow * vs X here? e.g. internal stop codons |
| 75 m = "".join("." if x == y else "!" for (x, y) in zip(p, t)) | |
| 0 | 76 if len(prot) < 70: |
| 77 sys.stderr.write("Protein: %s\n" % p) | |
| 78 sys.stderr.write(" %s\n" % m) | |
| 79 sys.stderr.write("Translation: %s\n" % t) | |
| 80 else: | |
| 81 for offset in range(0, len(p), 60): | |
| 3 | 82 sys.stderr.write("Protein: %s\n" % p[offset:offset + 60]) |
| 83 sys.stderr.write(" %s\n" % m[offset:offset + 60]) | |
| 84 sys.stderr.write("Translation: %s\n\n" % t[offset:offset + 60]) | |
| 85 sys.exit("Translation check failed for %s\n" % identifier) | |
| 86 | |
| 0 | 87 |
| 88 def sequence_back_translate(aligned_protein_record, unaligned_nucleotide_record, gap, table=0): | |
| 3 | 89 # TODO - Separate arguments for protein gap and nucleotide gap? |
| 0 | 90 if not gap or len(gap) != 1: |
| 91 raise ValueError("Please supply a single gap character") | |
| 92 | |
| 93 alpha = unaligned_nucleotide_record.seq.alphabet | |
| 94 if hasattr(alpha, "gap_char"): | |
| 95 gap_codon = alpha.gap_char * 3 | |
| 96 assert len(gap_codon) == 3 | |
| 97 else: | |
| 98 from Bio.Alphabet import Gapped | |
| 99 alpha = Gapped(alpha, gap) | |
| 3 | 100 gap_codon = gap * 3 |
| 0 | 101 |
| 102 ungapped_protein = aligned_protein_record.seq.ungap(gap) | |
| 103 ungapped_nucleotide = unaligned_nucleotide_record.seq | |
| 104 if table: | |
| 105 ungapped_nucleotide = check_trans(aligned_protein_record.id, ungapped_nucleotide, ungapped_protein, table) | |
| 106 elif len(ungapped_protein) * 3 != len(ungapped_nucleotide): | |
| 3 | 107 sys.exit("Inconsistent lengths for %s, ungapped protein %i, " |
| 0 | 108 "tripled %i vs ungapped nucleotide %i" % |
| 109 (aligned_protein_record.id, | |
| 110 len(ungapped_protein), | |
| 111 len(ungapped_protein) * 3, | |
| 112 len(ungapped_nucleotide))) | |
| 113 | |
| 114 seq = [] | |
| 115 nuc = str(ungapped_nucleotide) | |
| 116 for amino_acid in aligned_protein_record.seq: | |
| 117 if amino_acid == gap: | |
| 118 seq.append(gap_codon) | |
| 119 else: | |
| 120 seq.append(nuc[:3]) | |
| 121 nuc = nuc[3:] | |
| 122 assert not nuc, "Nucleotide sequence for %r longer than protein %r" \ | |
| 123 % (unaligned_nucleotide_record.id, aligned_protein_record.id) | |
| 124 | |
| 3 | 125 aligned_nuc = unaligned_nucleotide_record[:] # copy for most annotation |
| 126 aligned_nuc.letter_annotation = {} # clear this | |
| 127 aligned_nuc.seq = Seq("".join(seq), alpha) # replace this | |
| 0 | 128 assert len(aligned_protein_record.seq) * 3 == len(aligned_nuc) |
| 129 return aligned_nuc | |
| 130 | |
| 3 | 131 |
| 0 | 132 def alignment_back_translate(protein_alignment, nucleotide_records, key_function=None, gap=None, table=0): |
| 133 """Thread nucleotide sequences onto a protein alignment.""" | |
| 3 | 134 # TODO - Separate arguments for protein and nucleotide gap characters? |
| 0 | 135 if gap is None: |
| 136 gap = "-" | |
| 137 | |
| 138 aligned = [] | |
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139 try: |
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140 if key_function is None: |
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141 for protein in protein_alignment: |
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142 nucleotide = nucleotide_records[protein.id] |
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143 aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) |
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144 else: |
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145 for protein in protein_alignment: |
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146 nucleotide = nucleotide_records[key_function(protein.id)] |
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147 aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) |
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148 except KeyError: |
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149 raise ValueError("Could not find nucleotide sequence for protein %r" |
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150 % protein.id) |
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151 |
| 0 | 152 return MultipleSeqAlignment(aligned) |
| 153 | |
| 154 | |
| 155 if len(sys.argv) == 4: | |
| 156 align_format, prot_align_file, nuc_fasta_file = sys.argv[1:] | |
| 157 nuc_align_file = sys.stdout | |
| 158 table = 0 | |
| 159 elif len(sys.argv) == 5: | |
| 160 align_format, prot_align_file, nuc_fasta_file, nuc_align_file = sys.argv[1:] | |
| 161 table = 0 | |
| 162 elif len(sys.argv) == 6: | |
| 163 align_format, prot_align_file, nuc_fasta_file, nuc_align_file, table = sys.argv[1:] | |
| 164 else: | |
| 3 | 165 sys.exit("""This is a Python script for 'back-translating' a protein alignment, |
| 0 | 166 |
| 167 It requires three, four or five arguments: | |
| 168 - alignment format (e.g. fasta, clustal), | |
| 169 - aligned protein file (in specified format), | |
| 170 - unaligned nucleotide file (in fasta format). | |
| 171 - aligned nucleotiode output file (in same format), optional. | |
| 172 - NCBI translation table (0 for none), optional | |
| 173 | |
| 174 The nucleotide alignment is printed to stdout if no output filename is given. | |
| 175 | |
| 176 Example usage: | |
| 177 | |
| 178 $ python align_back_trans.py fasta demo_prot_align.fasta demo_nucs.fasta demo_nuc_align.fasta | |
| 179 | |
| 180 Warning: If the output file already exists, it will be overwritten. | |
| 181 | |
| 182 This script is available with sample data and a Galaxy wrapper here: | |
| 183 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans | |
| 184 http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans | |
| 185 """) | |
| 186 | |
| 187 try: | |
| 188 table = int(table) | |
| 3 | 189 except ValueError: |
| 190 sys.exit("Bad table argument %r" % table) | |
| 0 | 191 |
| 192 prot_align = AlignIO.read(prot_align_file, align_format, alphabet=generic_protein) | |
| 193 nuc_dict = SeqIO.index(nuc_fasta_file, "fasta") | |
| 194 nuc_align = alignment_back_translate(prot_align, nuc_dict, gap="-", table=table) | |
| 195 AlignIO.write(nuc_align, nuc_align_file, align_format) |