in reply to Very weird things when printing (may be an encoding issue?)

So, you have output from a variant caller or database. Have you had to parse data from the bot previously, or is this a one-off file? Some ideas:

1) Check the API documentation to see if it gives any hints.
2) Check if the output file was made on a Mac. You can try setting $/ = "\12"; at the beginning of the script to test (it changes the delimiter from \n to \r).

Bioinformatics

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Re^2: Very weird things when printing (may be an encoding issue?)
by dottornomade (Initiate) on May 30, 2013 at 10:21 UTC

    Thank you guys for the replies!

    Now I don't feel alone anymore.

    What I have to do is parse the file, retrieve the values and do some math.

    I opened the file with hex editor and found that odd lines end with "OA" (LineFeed), and even lines end with "OD" (CarriageReturn). And so here I am again, seeking for Perl wisdom at the monastery.

[reply]
      In that case, use the CR to separate the records and the LF to split into lines; 
      #!perl
use strict;
open IN,'<','weird.txt' or die "$!";
{
  local $/ = "\x0D";
  while (<IN>){
    my @lines = split /\x0A/;
    print $lines[0]."\n";
    print $lines[1]."\n\n";
  }
}

      [download]
      poj
[reply]
[d/l]

        It works.

        Hail to the Perl Monks!

        Seriously, thank you.

[reply]

      I opened the file with hex editor and found that odd lines end with "OA" (LineFeed), and even lines end with "OD" (CarriageReturn). And so here I am again, seeking for Perl wisdom at the monastery.

       perl -pi  -e " s/[\r\n]+/\n/g; " file
      dos2unix/Removing ^M char AKA dos2unix
      PerlIO::eol - PerlIO layer for normalizing line endings
      Text::FixEOL - Canonicalizes text to a specified EOL/EOF convention, repairing any 'mixed' usages
      File::LocalizeNewlines - Localize the newlines for one or more files

[reply]
[d/l]

In Section Seekers of Perl Wisdom