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|---|---|---|
| @@ -1,125 +1,128 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| def guess_alphabet(sequence): | ||
| """ | ||
| guess_alphabet(sequence) | ||
| returns an apropriate Biopython alphabet based on the content of the sequence. | ||
| >>> from pydna.dsdna import guess_alphabet | ||
| >>> guess_alphabet("aaa") | ||
| IUPACUnambiguousDNA() | ||
| >>> guess_alphabet("bbb") | ||
| IUPACProtein() | ||
| >>> guess_alphabet("aaaac") | ||
| IUPACUnambiguousDNA() | ||
| >>> guess_alphabet("agtc") | ||
| IUPACUnambiguousDNA() | ||
| >>> guess_alphabet("aguc") | ||
| IUPACUnambiguousRNA() | ||
| >>> guess_alphabet("ALAASN") | ||
| 'three letter code' | ||
| """ | ||
| # SeqRecord or Dseqrecord? | ||
| if hasattr(sequence, "features"): | ||
| sequence = str(sequence.seq) | ||
|
|
||
| # Seq or Dseq ? | ||
| elif hasattr(sequence, "reverse_complement"): | ||
| sequence = str(sequence) | ||
|
|
||
| else: | ||
| if not isinstance(sequence, str): | ||
| warnings.warn( | ||
| ("Input is {}, expected string, " "unicode string, Seq or SeqRecord " "objects!").format( | ||
| type(sequence) | ||
| ) | ||
| ) | ||
| sequence = str(sequence) | ||
|
|
||
| if len(sequence) < 1: | ||
| return SingleLetterAlphabet() | ||
|
|
||
| for c in sequence: | ||
| if c not in string.printable: | ||
| return SingleLetterAlphabet() | ||
|
|
||
| xp = set(extended_protein.letters) | ||
| pr = set(protein.letters) | ||
|
|
||
| ad = set(ambiguous_dna.letters) | ||
| ud = set(unambiguous_dna.letters) | ||
| ed = set(extended_dna.letters) | ||
|
|
||
| ar = set(ambiguous_rna.letters) | ||
| ur = set(unambiguous_rna.letters) | ||
|
|
||
| all = xp | pr | ad | ud | ed | ar | ur | ||
|
|
||
| sequence_chars = set(sequence.upper()) | ||
|
|
||
| if sequence_chars - all - set(string.punctuation + string.whitespace): | ||
| return SingleLetterAlphabet() | ||
|
|
||
| nucleic_count = 0 | ||
|
|
||
| for letter in "GATCUNgatcun": | ||
| nucleic_count += sequence.count(letter) | ||
|
|
||
| if float(nucleic_count) / float(len(sequence)) >= 0.9: # DNA or RNA | ||
| if "T" in sequence_chars and "U" in sequence_chars: | ||
| alphabet = NucleotideAlphabet() | ||
| elif not sequence_chars - ud: | ||
| alphabet = unambiguous_dna | ||
| elif not sequence_chars - ad: | ||
| alphabet = ambiguous_dna | ||
| elif not sequence_chars - ed: | ||
| alphabet = extended_dna | ||
| elif not sequence_chars - ur: | ||
| alphabet = unambiguous_rna | ||
| elif not sequence_chars - ar: | ||
| alphabet = extended_rna | ||
| else: | ||
| alphabet = NucleotideAlphabet() | ||
| else: | ||
| threecode = [ | ||
| "ALA", | ||
| "ASX", | ||
| "CYS", | ||
| "ASP", | ||
| "GLU", | ||
| "PHE", | ||
| "GLY", | ||
| "HIS", | ||
| "ILE", | ||
| "LYS", | ||
| "LEU", | ||
| "MET", | ||
| "ASN", | ||
| "PRO", | ||
| "GLN", | ||
| "ARG", | ||
| "SER", | ||
| "THR", | ||
| "VAL", | ||
| "TRP", | ||
| "TYR", | ||
| "GLX", | ||
| "XAA", | ||
| "TER", | ||
| "SEL", | ||
| "PYL", | ||
| "XLE", | ||
| ] | ||
| tc = set(threecode) | ||
| three_letter_alphabet = set([sequence[i : i + 3] for i in range(0, len(sequence), 3)]) | ||
| if not three_letter_alphabet - tc: | ||
| alphabet = "three letter code" | ||
| elif sequence_chars - pr: | ||
| alphabet = protein | ||
| elif sequence_chars - xp: | ||
| alphabet = extended_protein | ||
| else: | ||
| alphabet = ProteinAlphabet() | ||
| return alphabet | ||
| # #!/usr/bin/env python | ||
| # # -*- coding: utf-8 -*- | ||
|
|
||
|
|
||
| # def guess_alphabet(sequence): | ||
| # """ | ||
| # guess_alphabet(sequence) | ||
|
|
||
| # returns an apropriate Biopython alphabet based on the content of the sequence. | ||
|
|
||
| # >>> from pydna.dsdna import guess_alphabet | ||
| # >>> guess_alphabet("aaa") | ||
| # IUPACUnambiguousDNA() | ||
| # >>> guess_alphabet("bbb") | ||
| # IUPACProtein() | ||
| # >>> guess_alphabet("aaaac") | ||
| # IUPACUnambiguousDNA() | ||
| # >>> guess_alphabet("agtc") | ||
| # IUPACUnambiguousDNA() | ||
| # >>> guess_alphabet("aguc") | ||
| # IUPACUnambiguousRNA() | ||
| # >>> guess_alphabet("ALAASN") | ||
| # 'three letter code' | ||
|
|
||
| # """ | ||
| # # SeqRecord or Dseqrecord? | ||
| # if hasattr(sequence, "features"): | ||
| # sequence = str(sequence.seq) | ||
|
|
||
| # # Seq or Dseq ? | ||
| # elif hasattr(sequence, "reverse_complement"): | ||
| # sequence = str(sequence) | ||
|
|
||
| # else: | ||
| # if not isinstance(sequence, str): | ||
| # warnings.warn( | ||
| # ("Input is {}, expected string, " "unicode string, Seq or SeqRecord " "objects!").format( | ||
| # type(sequence) | ||
| # ) | ||
| # ) | ||
| # sequence = str(sequence) | ||
|
|
||
| # if len(sequence) < 1: | ||
| # return SingleLetterAlphabet() | ||
|
|
||
| # for c in sequence: | ||
| # if c not in string.printable: | ||
| # return SingleLetterAlphabet() | ||
|
|
||
| # xp = set(extended_protein.letters) | ||
| # pr = set(protein.letters) | ||
|
|
||
| # ad = set(ambiguous_dna.letters) | ||
| # ud = set(unambiguous_dna.letters) | ||
| # ed = set(extended_dna.letters) | ||
|
|
||
| # ar = set(ambiguous_rna.letters) | ||
| # ur = set(unambiguous_rna.letters) | ||
|
|
||
| # all = xp | pr | ad | ud | ed | ar | ur | ||
|
|
||
| # sequence_chars = set(sequence.upper()) | ||
|
|
||
| # if sequence_chars - all - set(string.punctuation + string.whitespace): | ||
| # return SingleLetterAlphabet() | ||
|
|
||
| # nucleic_count = 0 | ||
|
|
||
| # for letter in "GATCUNgatcun": | ||
| # nucleic_count += sequence.count(letter) | ||
|
|
||
| # if float(nucleic_count) / float(len(sequence)) >= 0.9: # DNA or RNA | ||
| # if "T" in sequence_chars and "U" in sequence_chars: | ||
| # alphabet = NucleotideAlphabet() | ||
| # elif not sequence_chars - ud: | ||
| # alphabet = unambiguous_dna | ||
| # elif not sequence_chars - ad: | ||
| # alphabet = ambiguous_dna | ||
| # elif not sequence_chars - ed: | ||
| # alphabet = extended_dna | ||
| # elif not sequence_chars - ur: | ||
| # alphabet = unambiguous_rna | ||
| # elif not sequence_chars - ar: | ||
| # alphabet = extended_rna | ||
| # else: | ||
| # alphabet = NucleotideAlphabet() | ||
| # else: | ||
| # threecode = [ | ||
| # "ALA", | ||
| # "ASX", | ||
| # "CYS", | ||
| # "ASP", | ||
| # "GLU", | ||
| # "PHE", | ||
| # "GLY", | ||
| # "HIS", | ||
| # "ILE", | ||
| # "LYS", | ||
| # "LEU", | ||
| # "MET", | ||
| # "ASN", | ||
| # "PRO", | ||
| # "GLN", | ||
| # "ARG", | ||
| # "SER", | ||
| # "THR", | ||
| # "VAL", | ||
| # "TRP", | ||
| # "TYR", | ||
| # "GLX", | ||
| # "XAA", | ||
| # "TER", | ||
| # "SEL", | ||
| # "PYL", | ||
| # "XLE", | ||
| # ] | ||
| # tc = set(threecode) | ||
| # three_letter_alphabet = set([sequence[i : i + 3] for i in range(0, len(sequence), 3)]) | ||
| # if not three_letter_alphabet - tc: | ||
| # alphabet = "three letter code" | ||
| # elif sequence_chars - pr: | ||
| # alphabet = protein | ||
| # elif sequence_chars - xp: | ||
| # alphabet = extended_protein | ||
| # else: | ||
| # alphabet = ProteinAlphabet() | ||
| # return alphabet |