CODEWITHSUNDEEP
perlcsvbioinformaticsstrict
Valentin Iglesias
Valentin Iglesias

Reputation: 11

Perl compilation error

sorry if it seems obvious but Im pretty new at Perl and programming and I've been working over a week and can't get it done. My idea is simple. I've got a .csv where I've got the names in the first column, a number from -1 to 1 in the second and a position on the third. Then another file where I have got the names (line starts with >) and the info with 80 characters per line.

What I want to do is keep the name lines of the first file and grab the 'position' given from -20 to +60. But I cannot get it to work and I've got to the point where don't know where to follow. 

use strict;                 #read file line by line
use warnings;
my $outputfile = "Output1.txt";
my $filename = "InputP.txt";
my $inputfasta = "Inputfasta.txt";
open my $fh, '<', $filename or die "Couldn't open '$filename'";
open my $fh2, '>', $outputfile or die "Couldn't create '$outputfile'";
open my $fh3, '<', $inputfasta or die "Couldn't open '$inputfasta'";
my $Psequence = 0;
my $seqname = 0;

while (my $line = <$fh>) {
chomp $line;
my $length = index ($line, ",");
$seqname = substr ($line, 0, $length);  

my $length2 = index ($line, ",", $length);
my $score = substr ($line, $length +1, $length2);   

my $length3 = index ($line, ",", $length2);
my $position = substr ($line, $length2 +1, $length3);   

#print $fh2 "$seqname"."\t"."$score"."\t"."$position"."\n";  }

my $Rlength2 = index ($score, ",");
my $Rscore = substr ($score, 0, $Rlength2);
#print "$Rscore"."\n";}
        while (my $linea = <$fh3>){  #same order.

            chomp $linea;
                if ($linea=~/^>(.+)/) { 
                    print $fh3 "\n"."$linea"."\n"; }
                else { $linea =~ /^\s*(.*)\s*$/;
                    chomp $linea;
                    print $fh3 "$linea". "\n"; }   
                    }
                if ($Rscore >= 0.5){
                    $Psequence = substr ($linea, -20, 81); 
                    print "$seqname"."\n"."$Psequence";}
        }

Upvotes: 1

Views: 67

Answers (2)

choroba
choroba

Reputation: 241898

Please, learn to indent the code correctly. Then the error will be more obvious:

while (my $linea = <$fh3>){  #same order.
    chomp $linea;
    if ($linea =~ /^>(.+)/) { 
        print $fh3 "\n$linea\n";
    } else {
        # Commented out as it does nothing.
        # $linea =~ /^\s*(.*)\s*$/;
        # chomp $linea;
        print $fh3 "$linea\n";
    }   
}

if ($Rscore >= 0.5){
    $Psequence = substr $linea, -20, 81; 
    print "$seqname\n$Psequence";
}

$linea exists only in the while loop, but you try to use it in the following paragraph, too. The variable disappears when the loop ends.

Upvotes: 3

ikegami
ikegami

Reputation: 385829

Create a hash from the CSV where the key is the name and the value is the position.

use Text::CSV_XS qw( );

my %pos_by_name;
{
   open(my $fh, '<', $input_qfn)
      or die("Can't open $input_qfn: $!\n");

   my $csv = Text::CSV_XS->new({ auto_diag => 1, binary => 1 });
   while (my $row = $csv_in->getline($fh)) {
      $pos_by_name{ $row->[0] } = $row->[2];
   }
}

Then, it's just a question of extracting the names from the other file, and using the hash to find the associated position.

open(my $fh, '<', $fasta_qfn)
   or die("Can't open $fasta_qfn: $!\n");

while (<$fh>) {
   chomp;
   my ($name) = /^>(.*)/
      or next;

   my $pos = $pos_by_name{$name};
   if (!defined($pos)) {
      die("Can't find position for $name\n");
   }

   ... Do something with $name and $pos ...
}

Upvotes: -1

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