SeqIO: “在句柄中未找到记录”

Question

我刚开始学习Python和BioPython，编程经验不多。希望大家能给我一些帮助。

我想从genbank中提取CDS和/或rRNA序列。因为我只想获取开放阅读框，所以我不想直接提取整个序列。当我运行下面的代码时，出现了一个错误，提示：

在处理过程中没有找到记录

这个错误出现在这行代码：record = SeqIO.read(handle, "genbank")。我不太确定该怎么解决这个问题。下面是我使用的代码。

另外，如果有更简单的方法或者已经发布的代码，麻烦告诉我一下。

谢谢！

# search sequences by a combination of keywords
# need to find (number of) results to set 'retmax' value
handle = Entrez.esearch(db = searchdb, term = searchterm)
records = Entrez.read(handle)
handle.close()
# repeat search with appropriate 'retmax' value
all_handle = Entrez.esearch(db = searchdb, term = searchterm, retmax = records['Count'])
records = Entrez.read(all_handle)

print " "
print "Number of sequences found:", records['Count'] #printing to make sure that code is working thus far. 
print " "

locations = [] # store locations of target sequences
sequences = [] # store target sequences

for i in range(0,int(records['Count'])) :
    handle = Entrez.efetch(db = searchdb, id = records['IdList'][i], rettype = "gb", retmode = "xml") 
    record = SeqIO.read(handle, "genbank")
    for feature in record.features:
        if feature.type==searchfeaturetype: #searches features for proper feature type
            if searchgeneproduct in feature.qualifiers['product'][0]: #searches features for proper gene product
                if str(feature.qualifiers) not in locations: # no repeat location entries
                    locations.append(str(feature.location)) # appends location entry
                    sequences.append(feature.extract(record.seq)) # append sequence

Answer 1

你在从genbank请求xml格式的数据，但SeqIO.read这个函数其实是期待你提供genbank的平面文件格式。试着把你的efetch这一行改成这样：

handle = Entrez.efetch(db = searchdb, id = records['IdList'][i], rettype = "gb", retmode = "txt")