使用python中的regex提取可变长度数

Question

I have a file in very bad shape but I am being able to parse it and extract most of the values required except one. And I need you help on how to regex to extract a variable length number.

To parse and extract other features I have used List indexes along with different spliiters '|', ' ' and ':'. But in this case I am being able to reach to block (below) and have to extract for each row the digits around '_' separately as x and y.

One way could be to first split by ':' and than by ' ' and finally by '-' but and extract index position [0] and [1] but that will be the most in-efficient way to do so.

chr5:17399789-17401949 REVERSE

chr5:6414488-6415907 FORWARD

chr5:2981156-2982709 FORWARD

chr5:6311725-6313323 REVERSE

chr5:12791432-12794551 REVERSE

chr5:927915-930781 FORWARD

chr5:19585936-19587841 FORWARD

chr5:26894856-26896488 FORWARD

chr5:18138775-18142147 REVERSE

chr5:20537525-20538943 REVERSE

chr5:22496196-22500543 REVERSE

chr5:4747860-4753592 REVERSE

The above block has come from 'bigger block' like this:

AT1G09410.1 | Symbols: | pentatricopeptide (PPR) repeat-containing protein | chr1:3035443-3037560 FORWARD

Can I extract at 'bigger block' also?

My programming level can be best describes as beginner and need you help.

Thanks

AK

Answer 1

One approach would be to define your regular expression as the following Python "raw" String:

    numericalBlockRegEx = r'chr\d+:(?P<firstNumBlock>\d+)-(?P<secondNumBlock>\d+)'

Finally, once you actually run your regular expression over each line of the file (you'll likely need to use a call to search rather than match) you can extract the numerical block you're interested in by a simple call to:

    x = match.group('firstNumBlock') #Gets first number block matched
    y = match.group('secondNumBlock') #Gets second number block matched

Cheers!