Question

我有一个问题，我需要从Genbank文件打印转换表。我的程序看起来像这样：

from Bio import SeqIO
record = SeqIO.read("mycoplasma.gb","genbank")
print record.id
print record.description
print "Number of features:", len(record.features)
ct=0
for f in record.features:
    if f.type=="tRNA":
        ct+=1
print "There are ", ct, "tRNa features"

ct2 = 0
for f in record.features:
    if f.type == "gene":
        ct2+=1
print "Therea are", ct2, "gene features"

ct3 = 0
for f in record.features:
    if f.type == "CDS":
        ct3+=1
print "There are", ct3, "CDS features"

print "The following is feature 4:"
print record.features[4]
print "The following information is about feature 21:"
print "It is a", record.features[21].type, "feature"
print "Its location is", record.features[21].location
for feature in record.features[21]:
    print feature.qualifiers["transl_table"]

我只需要最后一部分从文件中打印转换表。

Answer 1

这很容易。首先使用以下命令导入CodonTable：

from Bio.Data import CodonTable

之后你可以使用Genbank文件中的数字来获取CodonTables：

for feature in record.features:
    t_t = feature.qualifiers.get("transl_table")
        if t_t:
            print CodonTable.unambiguous_dna_by_id[int(t_t[0])]

请注意，您需要一个整数才能使用unambiguous_dna_by_id[]，而t_t很可能是['4']等字符串列表

使用BioPython从Genbank打印翻译表

1 个答案: