regex python:error: unmatched group

Question

I am a novice in python and have an issue using regex(). I have a parent directory and a subdirectory in it.

I'm using the regex(r'(.*/)?(.+/)(.+)\.bam')

to match the file with prefix '.bam' present in the subdirectory. A function utilizes the regex(), performs some task and gives the output and i need the output to be written to the parent directory.

Here is the total function which i am trying to do.

func(task,regex(r'(.*/)?(.+/)(.+)\.bam'),r'\1\3.output')

'.output' is the suffix to be added to the output and it shows the error "error: unmatched group". Could anyone help to fix this? or provide an elegant way to do this?

What is this regex function? Your regex compiles just fine. — Blender
– Blender, Commented May 30, 2013 at 17:06
actually the function is from a package Ruffus.Here is the original function: @transform(task, regex(r'(.*/)?(.+/(.+)\.bam'),r'\1\3.output'). This function takes in the inputfile from task which is of the format in the regex() and the suffix for output as '.output'. If i run the function from the parent directory it should take the input in subdir and should direct the output to parent dir. I doubt whether regex(r'(.*/)?(.+/)(.+)\.bam'),r'\1\3.output') does what in need? or im i going wrong? — chas
– chas, Commented May 30, 2013 at 17:42
Can you provide some sample text that you're searching in and the desired output? — Ro Yo Mi
– Ro Yo Mi, Commented May 30, 2013 at 18:38

Community · Accepted Answer · 2020-06-20 09:12:55Z

Description

This expression will pull the filename, the file's path, and the current folder's parent path.

((.*[\/])[^\/]*[\/])([^\/]*?)[.]bam

enter image description here

( start capture group 1
( start capture group 2
.*[\/] greedy match entire string upto...
) close capture group 2
[^\/]*[\/] require a the current directory
) close capture group 1
( start capture group 3
[^\/]*? non greedy match all non / characters before...
) close capture group 3
[.] require the dot character
bam require the bam value

Groups

Group 0 gets the entire string

gets the current path
gets the this folder's parent
gets the file name with .bam extension

Example

I don't know python well so here is a PHP example to show how this regex works.

$sourcestring="/ParentFolder1/SubFolder1/FileFoobar1.bam
/Some/Really/Deep/Folder/ParentFolder2/SubFolder2/FileFoobar2.bam";
preg_match_all('/((.*[\/])[^\/]*[\/])([^\/]*?)[.]bam/im',$sourcestring,$matches);
echo "<pre>".print_r($matches,true);
 
$matches Array:
(
    [0] => Array
        (
            [0] => /ParentFolder1/SubFolder1/FileFoobar1.bam
            [1] => /Some/Really/Deep/Folder/ParentFolder2/SubFolder2/FileFoobar2.bam
        )

    [1] => Array
        (
            [0] => /ParentFolder1/SubFolder1/
            [1] => /Some/Really/Deep/Folder/ParentFolder2/SubFolder2/
        )

    [2] => Array
        (
            [0] => /ParentFolder1/
            [1] => /Some/Really/Deep/Folder/ParentFolder2/
        )

    [3] => Array
        (
            [0] => FileFoobar1
            [1] => FileFoobar2
        )

)

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