写作列表CSV

Question

此代码

for record in SeqIO.parse(open(file, 'rU'), 'fasta', generic_protein): 
    record_id = re.sub(r'\d+_(\d+_\d\#\d+)_\d+', r'\1', record.id) 

    if (not reference_sequence): 
     reference_sequence = record.seq 
     reference_name  = record_id 
     #continue 
    print ",".join([reference_name, record_id, compare_seqs(reference_sequence, record.seq)]) 

使端子输出，看起来像

7065_8#1,8987_2#53, 
7065_8#1,8987_2#58, 
7065_8#1,8987_2#61, 
7065_8#1,8987_2#62,E-G [246] 
7065_8#1,8987_2#65,N-K [71],Y-D [223] 

我想通过线来写这条线到CSV，有什么建议？在嵌套列表

for record in SeqIO.parse(open(file, 'rU'), 'fasta', generic_protein): 
    record_id = re.sub(r'\d+_(\d+_\d\#\d+)_\d+', r'\1', record.id) 

if (not reference_sequence): 
    reference_sequence = record.seq 
    reference_name  = record_id 
    #continue 
line= ",".join([reference_name, record_id, compare_seqs(reference_sequence, record.seq)]) 
with open(csvfile, "w") as output: 
    writer = csv.writer(output, lineterminator='\n') 
    writer.writerow([line]) 

Answer 1

包中的所有记录（即代替print ','.join(...)你做records.append([...])），然后就可以使用writerows(records)，并写入到文件：

Answer 2

可以SUSE writerow与以下保存输出。不需要像'.'.join()这样的东西，这是csv为你做的。

为了完整起见：

records = [] 
for record in SeqIO.parse(open(file, 'rU'), 'fasta', generic_protein): 
    record_id = re.sub(r'\d+_(\d+_\d\#\d+)_\d+', r'\1', record.id) 

    if (not reference_sequence): 
     reference_sequence = record.seq 
     reference_name  = record_id 
     #continue 
    records.append([reference_name, record_id, compare_seqs(reference_sequence, record.seq)]) 

with csv.writer(open('file.csv', 'w')) as fp: 
    fp.writerows(records) # note that it's not writerow but writerows which allows you to write muptiple rows 

Answer 3

您也可以直接写逗号分隔字符串（与quotechar一起）的文件：

f = open("output.csv","w") 
for record in SeqIO.parse(open(file, 'rU'), 'fasta', generic_protein): 
    record_id = re.sub(r'\d+_(\d+_\d\#\d+)_\d+', r'\1', record.id) 

    if (not reference_sequence): 
    reference_sequence = record.seq 
    reference_name  = record_id 
    #continue 
    csvrow = '","'.join([reference_name, record_id, compare_seqs(reference_sequence, record.seq)]) 
    csvrow = '"'+csvrow+'"' 
    print >>f, csvrow 
f.close() 

使用这种方法，你可以打开文件并检查数据是否正在写入，即使脚本正在运行。