使用BioPython从Genbank打印翻译表
我有一个问题,我需要从Genbank文件打印翻译表。我的程序如下所示:使用BioPython从Genbank打印翻译表,python,biopython,Python,Biopython,我有一个问题,我需要从Genbank文件打印翻译表。我的程序如下所示: 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":
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来打印文件中的翻译表。很简单。首先使用以下内容导入CodonTables:
from Bio.Data import CodonTable
之后,您可以在Genbank文件中获得带有编号的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,您需要获得一个整数才能使用
无歧义的\u-dna\u-by\u-id[]
,t\u-t
很可能是一个字符串列表,如['4']
,您能否更明确地说明您需要帮助的问题是什么?