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#!/usr/bin/perl -p

...
        s/\s+\|/\|/g;
        s/(\d{2}:\d{2}:\d{2})\.\d+/$1/g;
        s/(\d{5})-(?:\d{1,4}|\s+)/$1/;

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```
my_scriptydoo.pl file1 > file2
```