<p>问题是,您将<em>id</em>添加到每个记录,而不仅仅是您感兴趣的记录。一个快速的解决方案是将<em>id</em>保持在一个变量中,并且只在必要时添加它:</p>
<pre><code>filename = 'C0_GGCTAC_R1_no_adapter_trimming.fastq'
new_filename = filename[:-9] + '_new.fastq'
with open(filename) as f_obj:
file_contents = f_obj.readlines()
extracted_lines = ''
line_count = 0
# Pull header and base lines
for line in file_contents:
line_count += 1
# Headers
if line_count == 1:
id_string = line
# Reads ending in A
elif line_count == 2 and line[-2] == 'A':
extracted_lines += id_string
extracted_lines += line
# Reads ending in G
elif line_count == 2 and line[-2] == 'G':
extracted_lines += id_string
extracted_lines += line
# Reset counter
elif line_count == 4:
line_count = 0
with open(new_filename, 'w') as f_obj:
f_obj.write(extracted_lines)
print(new_filename + " was created.")
</code></pre>
<p>我还不得不说,代码的效率不高,特别是在内存使用方面:您正在将一个(通常)非常大的文件读入内存,但一次只需要一条记录</p>
<p>第二个问题是可以压缩条件,并且可以使用模来了解所处的线型:</p>
<pre><code>filename = 'C0_GGCTAC_R1_no_adapter_trimming.fastq'
new_filename = filename[:-9] + '_new.fastq'
with open(filename) as in_f_obj, open(new_filename, 'w') as out_f_obj:
# Process the file
line_count = 0
for line in in_f_obj:
line_count += 1
# Extract the information for each record
if line_count % 4 == 1:
id_string = line
elif line_count % 4 == 2:
seq = line
elif line_count % 4 == 3:
extra = line
elif line_count % 4 == 4:
# Last part of the record. Here we have all the information
# and we can decide if we want to output something
# and what we want to output
qual = line
if seq[-2] == 'A' or seq[-2] == 'G'
out_f_obj.write(id_string)
out_f_obj.write(seq)
print(new_filename + " was created.")
</code></pre>
<p>在这段代码中,您只在内存中保留一条记录。<code>line_count</code>变量包含实际处理的行数,并且您拥有来自输入的所有数据,因此您可以很容易地在以后更改输出</p>
<p>我会添加一个额外的细节,我会在每一行中去掉换行符,并在写作时添加它(如果需要):</p>
<pre><code># Extract the information for each record
if line_count % 4 == 1:
id_string = line.rstrip()
elif line_count % 4 == 2:
seq = line.rstrip()
elif line_count % 4 == 3:
extra = line.rstrip()
elif line_count % 4 == 4:
# Last part of the record. Here we have all the information
# and we can decide if we want to output something
# and what we want to output
qual = line.rstrip()
if seq[-1] == 'A' or seq[-1] == 'G'
out_f_obj.write("{}\n{}\n".format(id_string, seq))
</code></pre>
<p>这样,您的数据是干净的,输入文件中没有新行格式</p>