寫作列表CSV

Question

此代碼

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)]) 

使端子輸出，看起來像

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] 

我想通過線來寫這條線到CSV，有什麼建議？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

包中的所有記錄（即代替print ','.join(...)你做records.append([...])），然後就可以使用writerows(records)，並寫入到文件：

Answer 2

可以SUSE writerow與以下保存輸出。不需要像'.'.join()這樣的東西，這是csv爲你做的。

爲了完整起見：

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

您也可以直接寫逗號分隔字符串（與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() 

使用這種方法，你可以打開文件並檢查數據是否正在寫入，即使腳本正在運行。