in reply to Re^4: Help with pushing into a hash
in thread Help with pushing into a hash

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

}

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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+(.+)
+/;
     }
 }

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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:

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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;

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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...

Replies are listed 'Best First'.
Re^6: Help with pushing into a hash
by jemswira (Novice) on Aug 31, 2012 at 15:43 UTC

    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 |

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    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.

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    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!

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      Ah! Excellent, jemswira!! Here's what's happening... The regex trys to capture everything past " | " for use as a value. However, in the lines above, there are no values, so $2 is not initialized for those lines which creates errors. To fix this, change the grep to:

      grep /\|\s+\S+/

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      You'll notice that the first part of the grep's regex is used in the map statement. The above adds \S+, which means that there need to be non-whitespace characters (i.e., values) beyond " | " for the line to pass. I'm assuming, here, that we can safely ignore lines that don't have anything past " | ". If this is the case, the above grep should resolve the errors.

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        Thanks. That removed 2 of the error lines. The first 2. Now these are left:

        
Use of uninitialized value $1 in hash element at C:\Users\Jems\Desktop
+\Perl\test\test2script.plx line 26.
Use of uninitialized value $1 in hash element at C:\Users\Jems\Desktop
+\Perl\test\test2script.plx line 27.
Use of uninitialized value $1 in hash element at C:\Users\Jems\Desktop
+\Perl\test\test2script.plx line 28.

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        lines 26, 27 and 28 are:

        for ( read_file $uniprot ) {
   /(.{6})\s+.+=([^\s]+)/;
    
    push @activline, "$1 | $2 | $activ{$1}\n" if $activ{$1}; #26
    push @antioxline, "$1 | $2 | $antiox{$1}\n" if $antiox{$1}; #27
    push @toxinline, "$1 | $2 | $toxin{$1}\n" if $toxin{$1};#28

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        The format for $uniprot is the same as for $test. I.E.

        Q197F8 ORFNames=IIV3-002R 
Q197F7 ORFNames=IIV3-003L 
Q6GZX2 ORFNames=FV3-003R 
Q6GZX1 ORFNames=FV3-004R 
Q197F5 ORFNames=IIV3-005L
Q6GZX0 ORFNames=FV3-005R ;PF02393
Q91G88 ORFNames=IIV6-006L ;PF12299;PF04383
Q6GZW9 ORFNames=FV3-006R

        [download]

        Thanks again!

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