biopython - 将 FASTA 转换为 GenBank

Question

有没有办法使用 BioPython 将 FASTA 文件转换为 Genbank 格式？关于如何从 Genbank 转换为 FASTA 有很多答案，但反之则不然。

Answer 1

在转换之前，您必须将字母表分配给序列(DNA 或蛋白质)

from Bio import SeqIO
from Bio.Alphabet import generic_dna, generic_protein

input_handle = open("test.fasta", "rU")
output_handle = open("test.gb", "w")

sequences = list(SeqIO.parse(input_handle, "fasta"))

#asign generic_dna or generic_protein
for seq in sequences:
  seq.seq.alphabet = generic_dna

count = SeqIO.write(sequences, output_handle, "genbank")

output_handle.close()
input_handle.close()
print "Coverted %i records" % count

输入:

>I28Q9A102FII8J rank=0668881 x=2144.0 y=1105.0 length=418ACGTCATGAGAGTTTGATCATGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGATGAAGCTCCAGCTTGCTGGGGTGGATTAGTGGCGAACGGGTGAGTAACACGTGAGTAACCTGCCCTTGACTCTGGGATAAGCGTTGGAAACGACGTCTAATACCGGATATGACGACCGATGGCATCATCTGGTTGTGGAAAGAATTTTGGTCAAGGATGGACTCGCGGCCTATCAGGTAGTTGGTGAGGTAATGGCTCACCAAGCCTACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGAAAGCCTGATGCAGCAACGCCGCGTGAGGGATGACGGCC>I28Q9A102JMH72 rank=0320459 x=3829.0 y=3120.0 length=512ACGTCATGAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGTAGAAATAGCTTGCTATTTTGAGACCGGCGCACGGGTGCGTAACGCGTATGCAATCTGCCTTTTACAGGGGAATAGCCCAGAGAAATTTGGATTAATGCCCCATAGCGCTGCAGGGCGGCATCGCCGAGCAGCTAAAGTCACAACGGTAAAGATGAGCATGCGTCCCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCGATGATGGGTAGGGTCCTGAGAGGGAGATCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGCAAGCCTGAACCAGCCATGCCGCGTGCAGGATGAAGGCCTTCGGGTTGTAAACTGCTTTTGACGGAACGAAAAAGCT

你得到:

LOCUS       I28Q9A102FII8J           418 bp    DNA              UNK 01-JAN-1980DEFINITION  I28Q9A102FII8J rank=0668881 x=2144.0 y=1105.0 length=418ACCESSION   I28Q9A102FII8JVERSION     I28Q9A102FII8JKEYWORDS    .SOURCE      .  ORGANISM  .            .FEATURES             Location/QualifiersORIGIN        1 acgtcatgag agtttgatca tggctcagga cgaacgctgg cggcgtgctt aacacatgca       61 agtcgaacga tgaagctcca gcttgctggg gtggattagt ggcgaacggg tgagtaacac      121 gtgagtaacc tgcccttgac tctgggataa gcgttggaaa cgacgtctaa taccggatat      181 gacgaccgat ggcatcatct ggttgtggaa agaattttgg tcaaggatgg actcgcggcc      241 tatcaggtag ttggtgaggt aatggctcac caagcctacg acgggtagcc ggcctgagag      301 ggtgaccggc cacactggga ctgagacacg gcccagactc ctacgggagg cagcagtggg      361 gaatattgca caatgggcga aagcctgatg cagcaacgcc gcgtgaggga tgacggcc//LOCUS       I28Q9A102JMH72           450 bp    DNA              UNK 01-JAN-1980DEFINITION  I28Q9A102JMH72 rank=0320459 x=3829.0 y=3120.0 length=512ACCESSION   I28Q9A102JMH72VERSION     I28Q9A102JMH72KEYWORDS    .SOURCE      .  ORGANISM  .            .FEATURES             Location/QualifiersORIGIN        1 acgtcatgag agtttgatcc tggctcagga tgaacgctag cggcaggctt aacacatgca       61 agtcgagggt agaaatagct tgctattttg agaccggcgc acgggtgcgt aacgcgtatg      121 caatctgcct tttacagggg aatagcccag agaaatttgg attaatgccc catagcgctg      181 cagggcggca tcgccgagca gctaaagtca caacggtaaa gatgagcatg cgtcccatta      241 gctagttggt aaggtaacgg cttaccaagg cgatgatggg tagggtcctg agagggagat      301 cccccacact ggtactgaga cacggaccag actcctacgg gaggcagcag tgaggaatat      361 tggtcaatgg gcgcaagcct gaaccagcca tgccgcgtgc aggatgaagg ccttcgggtt      421 gtaaactgct tttgacggaa cgaaaaagct//