This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Perl Blast Output Counting Program

Hello Internet...I need help...

I am trying to write a perl script to take a BLASTp .txt output file containing the top 100 hits for each protein sequence in a genome and process some simple information from the file.

Currently the program is adding one to a value in each row of the first column for each time it finds one of the desired hits and one to the second column for each non-hit. It is not recognizing each protein correctly and it is giving me a sum total for the whole file. What I essential want to know for each protein is how many hits have been recorded, how many of those hits are to a particular phylum (Elusimicrobia), and how many are not to that phylum and naturally the gene name in the first column but all consolidated into one row.

PLEASE HELP!!! THANK YOU!!

#!/usr/bin/perl
use warnings;

die "usage: <count_elusi_hits>\n" unless @ARGV == 2;
$inputfile = $ARGV[0];  # blast.out
$outputfile = $ARGV[1]; # hit counts

open(IN, $inputfile) or die " Something went wrong! Check your 1st input file";
open(OUT, ">$outputfile");

%hit_hash = ();
$elusi_hits = 0;
$non_elusi_hits = 0;

print OUT "Elusimicrobia Hit    Non-Elusi Hits\n";

while ($line= <IN>){
chomp $line;

@array = split (/\t/, $line); #split at tab, make array

$hit_hash{$array[0]}= $array[1];
    #print "$_\n" for keys %hit_hash;
    #print "$hit_hash{$array[0]}\n";
    #}
for $keys (keys %hit_hash){
    if ($hit_hash{$array[0]} =~ /Elusi*|Endomicrobium*|Termite group 1*|TG1*/){
    $elusi_hits += +1;
        }
        else{
        $non_elusi_hits += +1;
        }

print OUT "$elusi_hits  $non_elusi_hits\n";
}
}
 close IN;
 close OUT;
 exit;

Input file looks something like this with ~1000 blasted proteins and roughly 77,000 hit proteins:

Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Candidatus Endomicrobium trichonymphae]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  enolase [Candidatus Endomicrobium trichonymphae]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Endomicrobium proavitum]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFOXYA12_FULL_49_49]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFOXYA2_FULL_40_6]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFOXYA2_FULL_50_26]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFOXYA2_FULL_39_19]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium CG1_02_37_114]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFOXYB2_FULL_48_7]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium HGW-Elusimicrobia-1]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFCSPLOWO2_01_FULL_59_12]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Desulfuromonas sp.]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium GWA2_38_7]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Desulfuromonas sp.]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFOXYD2_FULL_34_15]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Geoalkalibacter ferrihydriticus]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Pelobacter carbinolicus]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Geopsychrobacter electrodiphilus]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Desulfuromonas sp.]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Desulfobacteraceae bacterium 4572_35.1]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Pelobacter acetylenicus]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium CG06_land_8_20_14_3_00_38_11]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Brevibacillus laterosporus]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Desulfuromonadales bacterium C00003068]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Brevibacillus laterosporus]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Malonomonas rubra]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Brevibacillus laterosporus]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Elusimicrobia bacterium RIFOXYC2_FULL_34_12]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Idiomarina salinarum]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Pelobacter seleniigenes]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Desulfuromonas sp.]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Desulfuromonas sp.]
Endomicrobium_sp_ds12|_fig|6666666.252603.peg.2_|_scaffold1.1_1490_186_|_Enolase_(EC_4.2.1.11)  phosphopyruvate hydratase [Succinivibrio dextrinosolvens]
perl counting software error blast
• 1,555 views • link
updated by lieven.sterck 1.6K • | written by shane.hussey 0

1 answer

I changed your while loop a little, following code should give you what you want:

while ($line= <IN>){
   chomp $line;
   @array = split (/\t/, $line); #split at tab, make array

    if ( $array[1] =~ /Elusi*|Endomicrobium*|Termite group 1*|TG1*/){
                $hit_hash{$array[0]}{'hits'}++;
    }
    else{
                $hit_hash{$array[0]}{'noHits'}++;
    }
}
close IN;

foreach $key (keys %hit_hash){
        print OUT "$key $hit_hash{$key}{'hits'}  $hit_hash{$key}{'noHits'}\n";
}
close OUT;
exit;

one last suggestion: always use use strict when coding in PERL, you will then need to declare your variables but it's well worth the effort

• 0 views • link
written by lieven.sterck 1.6K

Log in to answer this question.

More posts like this

No similar posts found.