perl progrmme error for blast tab limited out put Parsing

Question: (Closed) perl progrmme error for blast tab limited out put Parsing

4.0 years ago by

akhilvbioinfo • 140

India, chennai

akhilvbioinfo • 140 wrote:

use warnings;

print "Enter Your BLAST result file name:\t";
chomp($blast = <STDIN>); # BLAST result file name
print "\n";

print "Enter Your Gene list file name:\t";
chomp($database = <STDIN>); # file name
print "\n";

open IN,"$blast" or die "Can not open file $blast: $!";

@ids = ();
@seq_start = ();
@seq_end = ();

while(<IN>){

@feilds = split("\t",$_);
push(@ids,$feilds[0]);
push(@seq_start,$feilds[6]);
push(@seq_end,$feilds[7]);
}
close IN;

open OUT,">Result.fasta" or die "Can not open file $database: $!";

for($i=0;$i<=$#ids;$i++){

($sequence) = &block($ids[$i]);

($idline,$sequence) = split("\n",$sequence);

   if($seq_start[$i] <= 70){
   $pos_Start = 0;
   }
   else{
   $pos_Start = $seq_start[$i]-70;
   }

   $pos_end = $seq_end[$i]+70;
   if($pos_end >= length($sequence)){
   $pos_end = length($sequence);
   }

$seqlen = $pos_end - $pos_Start;

$Nucleotides = substr($sequence,$pos_Start,$seqlen);

$Nucleotides =~ s/(.{1,60})/$1\n/gs;

print OUT "$idline\n";
print OUT "$Nucleotides\n";
}
print "\nExtraction Completed...";

sub block{

$id1 =shift;
print "$id1\n";
$start = ();

open IN3,"$database" or die "Can not open file $database: $!";

$blockseq = "";
while(<IN3>){

   if (($_ =~ /^>/)&&($start)){

   last;
   }

   if (($_ !~ /^>/)&&($start)){

   chomp;
   $blockseq .= $_;
   }

   if (/^>$id1/){

   $start = $.;print "$.\n";#-1;
   $blockseq .= $_;
   }
}
close IN3;

return($blockseq);
}<STDIN>;

I got following errors while running the above code

Use of uninitialized value $seq_start[1] in numeric le (<=) at Blast_Extractor1.pl line 35.

Use of uninitialized value $seq_end[1] in addition (+) at Blast_Extractor1.pl line 42.

Use of uninitialized value in numeric ge (>=) at Blast_Extractor1.pl line 43.

Use of uninitialized value $pos_end in subtraction (-) at Blast_Extractor1.pl line 47.

Use of uninitialized value $sequence in substr at Blast_Extractor1.pl line 49.

Use of uninitialized value $idline in concatenation (.) or string at Blast_Extractor1.pl line 53.

blast perl • 1.2k views

ADD COMMENT • link •

modified 4.0 years ago by Michael Dondrup ♦ 46k • written 4.0 years ago by akhilvbioinfo • 140

GCA_001188035.1_1       GCA_001188035.1_1       100.00  159     0       0       1       159     1       159     8e-113   324

GCA_001188035.1_1       GCF_000878595.1_1595    100.00  159     0       0       1       159     853     1011    2e-104   327

GCA_001188035.1_1       GCA_001267965.1_78      100.00  159     0       0       1       159     853     1011    2e-104   327

GCA_001188035.1_1       GCF_000568495.1_4683    100.00  159     0       0       1       159     853     1011    2e-104   327

GCA_001188035.1_2       GCF_000568495.1_4684    100.00  137     0       0       1       137     1       137     8e-97    281

GCA_001188035.1_2       GCA_001188035.1_2       100.00  137     0       0       1       137     1       137     8e-97    281

this is my blast out put

ADD REPLY • link written 4.0 years ago by akhilvbioinfo • 140

Hello akhilvbioinfo!

We believe that this post does not fit the main topic of this site.

This is a pure Perl question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLY • link written 4.0 years ago by RamRS ♦ 24k

4.0 years ago by

Michael Dondrup ♦ 46k

Bergen, Norway

Michael Dondrup ♦ 46k wrote:

These are not errors but warnings, more often then not they are caused but a non-defensive programming style. The following mistakes were made in the above code:

it exists: you wrote a blast parser yourself while there are libraries
you did not use strict;
good code handles blank lines and comments, this one doesn't, most likely the reason for all warnings
you do not chomp
you use a error prone for loop where foreach could be applied instead of $#ids
you silently assume that each line has at least 7 entries but you never verify that, so you are pushing undef's onto an array
you do not check if these entries are numeric

ADD COMMENT • link modified 4.0 years ago • written 4.0 years ago by Michael Dondrup ♦ 46k

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