从python 2.7.5中的文本文件中提取字符串

Question

Hello I am new to python, and I hope you can help me. I have a text file (call it data.txt) with data on gene number with corresponding rs number and some distance measure. The data looks something like this:

   rs1982171     55349     40802

   rs6088650     55902     38550

   rs1655902     3105      12220

   rs1013677     55902      0

where the first column is rs number, second column is gene number, and third column is some distance measure. The data is much bigger, but hopefully the above gives you an idea of the dataset. What I want to do is find all the rs numbers that correspond to a certain gene. For example, for the data set above, gene 55902= {rs6088650, rs1013677}. Ideally, I want my code to find all rs numbers corresponding to a given gene. Since I am unable to do that now, I instead wrote a short code that gives the lines that contain the string "55902" in the data.txt file:

  import re
  data=open("data.txt","r")
  for line in data:
      line=line.rstrip()
      if re.search("55902",line):
      print line

The problem with this code is that the output is something like this:

    rs6088650    55902     38550

    rs1655902    3105      12220

    rs1013677    55902     0

I want my code to ignore the string "55902" in the rs number. In other words, I don't my code to output the second line in the above output because the gene number is not 55902. I would like my output to be :

       rs6088650     55902   38550

       rs1013677     55902   0

How can I modify the above code to achieve what I want. Any help would be appreciated. Thanks in advance.

Answer 1

You can use word boundary ( \\b ) , to match whole word search:

>>> import re
>>> re.search(r"\b55902\b", "rs1655902     3105      12220")
>>> re.search(r"\b55902\b", "rs6088650     55902     38550")
<_sre.SRE_Match object at 0x7f82594566b0>

---

if re.search(r"\b55902\b", line):
    ....

Answer 2

You can do this easily with a more powerful regular expression. One possible quick solution is to use a regex of the form:

r'\b55902\b'

The \\b are word boundaries.

Answer 3

There's no need for regular expressions here, as all you're looking for is a simple static sequence. This line:

if re.search("55902",line):

Could be expressed as:

if "55902" in line:

And if you only want to check the second column, split the line first:

if '55902' in line.split()[1]:

Since you're now already checking the correct column, check for equality rather than membership:

if line.split()[1] == '55902':

Answer 4

If you want to use regex , then you can use match or search along with word boundary \\b as

x = "   rs1982171     55349     40802".strip()

if (re.match(r"\b55349\b", x.split()[1])):
    print x

IDEONE DEMO