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  • One-liner to parse 454BaseCallerMetrics.txt

    After processing usually follows the maddeningly slow crawl through 454BaseCallerMetrics.txt to find out whether it is a good day or not. Typically I egrep for a few keywords (eg "totalBases") to get an idea. But, even then I am squinting at the screen, counting digits to see if all went well. How about a nice perl one-liner that will pull the lines of interest and add commas in the right places in long numbers?

    Code:
    perl -ne 's/(\d)(?=(\d{3})+(\D|$))/$1\,/g; print if /region|numberReads|totalBases|average|key/;' 454BaseCallerMetrics.txt

    That sweet "insert commas into numbers" regex courtesy of Randall Schwartz:



    --
    Phillip
    Last edited by pmiguel; 07-26-2011, 06:25 AM. Reason: Changed "averageLength" to "average"

  • #2
    By the way, my take on how the regex functions is:

    Code:
    s{
        (\d)            #capture a single digit
        (?=            #so-called look ahead assertion
           (\d{3})+ #3 digits -- remember greediness, though!
           (\D|$)     #a single "not a digit" or end of string (line)
        )
    }
    {$1\,}gx
    #replace the first captured digit with itself plus a comma -- repeat until the end of the string is reached
    The goofy "(?=)" syntax requires the regex inside be true, but does not actually "consume" the characters it matches.

    One other factor in play: most repeat regex operators are naturally "greedy". That is, they try to match as much as possible. So \d{3}+ will match as many instances as possible of groups of three digits. The result is that the first comma to be replaced is the leftward-most one.

    The "g", of course, calls for the matching to be repeated until the end of the string is reached. This is where the (?=) becomes important. Even though it matched all the way to the end of the number, it is a "zero width assertion", meaning string matching picks up again right where the (?=) had started. Hence the next comma can be insert, and so on.

    --
    Phillip

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