Python正则表达式-将两个单词之间的文本捕获为字符串，然后追加到列表中

Question

This is the structure of the txt file (repeated units of CDS-text-ORIGIN):

     CDS             311..>428
                     /gene="PNR"
                     /codon_start=1
                     /product="photoreceptor-specific nuclear receptor"
                     /protein_id="AAD28302.1"
                     /db_xref="GI:4726077"
                     /translation="METRPTALMSSTVAAAAPAAGAASRKESPGRWGLGEDPT"
 ORIGIN

I want to pull out the text from 311..<428 to GEDPT" as a string The regex I have so far is:

compiler = re.compile(r"^\s+CDS\s+(.+)ORIGIN.+", re.DOTALL|re.MULTILINE)

I then use a loop to add each string to a list:

for line in file:
    match = compiler.match(line)
    if match:
        list.append(str(match.group(1)))

But I keep getting an empty list! Any ideas why?

Help would be much appreciated, I'm new to this!

Answer 1

I am assuming that file is a filepointer such as file = open('filename.txt') . If that is the case then using:

for line in file:

will break each line on the newline character. So the first three lines will be:

1: '     CDS             311..>428\n'
2: '                     /gene="PNR"\n'
3: '                     /codon_start=1:\n'

Because each line is separate, you will not match the multiline pattern unless you combine the lines. You may want to consider using:

compiler = re.compile(r"^\s+CDS\s+(.+?)ORIGIN", re.DOTALL|re.MULTILINE)
fp = open('filename.txt')
all_text = fp.read()         # this reads all the text without splitting on newlines
compiler.findall(all_text)   # returns a list of all matches