Есть ли способ использовать BioPython для преобразования файлов FASTA в формат Genbank? Есть много ответов о том, как перейти с Genbank на FASTA, но не наоборот.
Конвертировать FASTA в GenBank
Ответы (1)
перед преобразованием вы должны назначить алфавит последовательности (ДНК или белок)
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
для ввода:
>I28Q9A102FII8J rank=0668881 x=2144.0 y=1105.0 length=418 ACGTCATGAGAGTTTGATCATGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGATGAA GCTCCAGCTTGCTGGGGTGGATTAGTGGCGAACGGGTGAGTAACACGTGAGTAACCTGCCCTTGACTCTGGGAT AAGCGTTGGAAACGACGTCTAATACCGGATATGACGACCGATGGCATCATCTGGTTGTGGAAAGAATTTTGGTC AAGGATGGACTCGCGGCCTATCAGGTAGTTGGTGAGGTAATGGCTCACCAAGCCTACGACGGGTAGCCGGCCTG AGAGGGTGACCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCA CAATGGGCGAAAGCCTGATGCAGCAACGCCGCGTGAGGGATGACGGCC >I28Q9A102JMH72 rank=0320459 x=3829.0 y=3120.0 length=512 ACGTCATGAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGTAGAA ATAGCTTGCTATTTTGAGACCGGCGCACGGGTGCGTAACGCGTATGCAATCTGCCTTTTACAGGGGAATAGCCC AGAGAAATTTGGATTAATGCCCCATAGCGCTGCAGGGCGGCATCGCCGAGCAGCTAAAGTCACAACGGTAAAGA TGAGCATGCGTCCCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCGATGATGGGTAGGGTCCTGAGAGGG AGATCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGG GCGCAAGCCTGAACCAGCCATGCCGCGTGCAGGATGAAGGCCTTCGGGTTGTAAACTGCTTTTGACGGAACGAA AAAGCT
ты получаешь:
LOCUS I28Q9A102FII8J 418 bp DNA UNK 01-JAN-1980 DEFINITION I28Q9A102FII8J rank=0668881 x=2144.0 y=1105.0 length=418 ACCESSION I28Q9A102FII8J VERSION I28Q9A102FII8J KEYWORDS . SOURCE . ORGANISM . . FEATURES Location/Qualifiers ORIGIN 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-1980 DEFINITION I28Q9A102JMH72 rank=0320459 x=3829.0 y=3120.0 length=512 ACCESSION I28Q9A102JMH72 VERSION I28Q9A102JMH72 KEYWORDS . SOURCE . ORGANISM . . FEATURES Location/Qualifiers ORIGIN 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 //
person
Jose Ricardo Bustos M.
schedule
12.05.2015