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Re^2: Help with pushing into a hash

by jemswira (Novice)
on Aug 30, 2012 at 11:32 UTC ( #990721=note: print w/ replies, xml ) Need Help??


in reply to Re: Help with pushing into a hash
in thread Help with pushing into a hash

Thanks so much! It works like a charm. On a side note, how do I remove the decimal place. I tried using (PF.{5}) instead of the (.+) but it would only return the last PF value and nothing else.


Comment on Re^2: Help with pushing into a hash
Re^3: Help with pushing into a hash
by Anonymous Monk on Aug 30, 2012 at 11:39 UTC

    Ask yourself what you want to match?

    In regular expression dot means any character

      Well I want to match all the PF.{5} but i don't want the decimal point at the end, and the numbers after the decimal point. So essentially I want to match all the PF.{5} only.

        Well I want to match all the PF.{5} but i don't want the decimal point at the end, and the numbers after the decimal point. So essentially I want to match all the PF.{5} only.

        What does that mean?

        I have a better idea, post your changed code, the thing that isn't working

Re^3: Help with pushing into a hash
by Kenosis (Priest) on Aug 30, 2012 at 17:16 UTC

    You're welcome, jemswira!

    To remove the decimal values in the test2.txt data, try changing the following:

    my %data = map { /(.+)\s+\|\s+(.+)/; $1 => $2 } read_file $test2;

    to:

    my %data = map {s/\.\d+//g; /(.+)\s+\|\s+(.+)/; $1 => $2 } read_file $ +test2;

    New output to file:

    Q197F8 IIV3-002R PF04947 Q91G88 IIV6-006L PF01486 PF00319

    The substitution at the beginning of the map block will globally remove a decimal point followed by one or more digits. Since only the test2.txt values (not keys) contain decimal points, this should work.

      Thank again Kenosis (bows)

      Well I used the code you gave me and tweaked it abit so it could do multiple files at one time so I didnt have to load the hash everytime I wanted to do multiple files. But it returns the errors:

      Use of uninitialized value in list assignment at C:\Users\Jems\Desktop +\Perl\test\test2script.plx line 20. Use of uninitialized value in list assignment at C:\Users\Jems\Desktop +\Perl\test\test2script.plx line 22. Use of uninitialized value in list assignment at C:\Users\Jems\Desktop +\Perl\test\test2script.plx line 26. Use of uninitialized value in list assignment at C:\Users\Jems\Desktop +\Perl\test\test2script.plx line 27. Use of uninitialized value in list assignment at C:\Users\Jems\Desktop +\Perl\test\test2script.plx line 28.

      Also, the when I run it in Padre, it gives the popup message

      line 39: Substitute(s///) doesnt return the changed value even if map.  Continue? Y/N.

      What is wrong with my code?

      #!/usr/bin/perl use Modern::Perl; use File::Slurp qw/read_file write_file/; my $uniprot = 'uniprot-sfinal.txt'; my $activin = 'Activator-PFAM.txt'; my $antioxin = 'AntiOxidant-PFAM.txt'; my $toxinin= 'Toxin-PFAM.txt'; my $activout = 'ActivACNPF.txt'; my $antioxout= 'AntioxACNPF.txt'; my $toxinout= 'ToxinACNPF.txt'; my @activline; my @antioxline; my @toxinline; my %activ = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/; $1 => $2 } read_fil +e $activin; my %antiox = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/; $1 => $2 } read_fil +e $antioxin; my %toxin = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/; $1 => $2 } read_fil +e $toxinin; for ( read_file $uniprot ) { /(.{6})\s+.+=([^\s]+)/; push @activline, "$1 | $2 | $activ{$1}\n" if $activ{$1}; push @antioxline, "$1 | $2 | $antiox{$1}\n" if $antiox{$1}; push @toxinline, "$1 | $2 | $toxin{$1}\n" if $toxin{$1}; } write_file $activout, @activline; write_file $antioxout, @antioxline; write_file $toxinout, @toxinline;

      The input format is still the same as before, but just more input.

        You're most welcome, jemswira! (And, if you need to bow, bow only to Perl... :)

        The errors suggest a failed regex in one or more of the map statements. Here are the lines where the errors occurred:

        my %activ = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/; $1 => $2 } read_fil +e $activin; # Line 20 my %antiox = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/; $1 => $2 } read_fil +e $antioxin; # Line 21 my %toxin = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/; $1 => $2 } read_fil +e $toxinin; # Line 22 for ( read_file $uniprot ) { # Line 23 /(.{6})\s+.+=([^\s]+)/; # Line 24 push @activline, "$1 | $2 | $activ{$1}\n" if $activ{$1}; # Line 2 +6 push @antioxline, "$1 | $2 | $antiox{$1}\n" if $antiox{$1}; # Lin +e 27 push @toxinline, "$1 | $2 | $toxin{$1}\n" if $toxin{$1}; # Line 2 +8 }

        Sounds like there may be lines in the files with differently-formatted data that the regex fails to match. To see if this is the case, try the following:

        for my $file (qw/Activator-PFAM.txt AntiOxidant-PFAM.txt Toxin-PFAM.tx +t/){ for(read_file $file){ say "No Match in File: $file; Line: $_" if !/(.+)\s+\|\s+(.+) +/; } }

        This will go through each file and display any line the regex doesn't match. If lines with data on them show, the regex will need to be adjusted. If empty lines show, e.g.,:

        No Match in File: test2.txt; Line:

        Try adding a grep before the file read that allows only non-blank lines to pass. For example:

        my %data = map {s/\.\d+//g; /(.+)\s+\|\s+(.+)/ and $1 => $2 } grep /\S +/, read_file $test2;

        If no lines show, I'm not sure what the issue may be. In any case, however, please get back to me or the Monks...

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