Beefy Boxes and Bandwidth Generously Provided by pair Networks
more useful options
 
PerlMonks  

Re^3: Help with pushing into a hash

by Kenosis (Priest)
on Aug 30, 2012 at 17:16 UTC ( #990801=note: print w/ replies, xml ) Need Help??


in reply to Re^2: Help with pushing into a hash
in thread Help with pushing into a hash

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.


Comment on Re^3: Help with pushing into a hash
Select or Download Code
Re^4: Help with pushing into a hash
by jemswira (Novice) on Aug 31, 2012 at 11:48 UTC

    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...

        Thanks again! I ran the check and had some blank lines:

        No Match in File: Activator-PFAM.txt; Line: Q8UPQ0 | No Match in File: Toxin-PFAM.txt; Line: Q306M5 |

        So i added the grep before the file read, and the error changed.

        Odd number of elements in hash assignment at C:\Users\Jems\Desktop\Per +l\test\test2script.plx line 20. Odd number of elements in hash assignment at C:\Users\Jems\Desktop\Per +l\test\test2script.plx line 22. Odd number of elements in hash assignment at C:\Users\Jems\Desktop\Per +l\test\test2script.plx line 26. Odd number of elements in hash assignment at C:\Users\Jems\Desktop\Per +l\test\test2script.plx line 27. Odd number of elements in hash assignment at C:\Users\Jems\Desktop\Per +l\test\test2script.plx line 28.

        Still same lines. And somehow line 21, which was for the file that did not give the error still did not give the error. Also Padre is warning me that the substitution will not replace anything.

        thanks!

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://990801]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others surveying the Monastery: (6)
As of 2014-10-25 06:04 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    For retirement, I am banking on:










    Results (142 votes), past polls