Hi beherasan,

I'm hoping that you're able to run on a Unix platform. If yes, there's a way to run without consuming lots of memory. Imagine that :) There is a fast database named Kyoto Cabinet. It is quite fast. See more info here and here, on PerlMonks. The latter provides installation instructions.

This post was made for folks not having access to the gigantic Fasta file or would rather generate something on the fly. I shuffle the bits in order to have unique records. The OP will not need these scripts and can skip to Part Three over here.

Part One create fake Fasta file for simulation (144 MiB)

# https://www.perlmonks.org/?node_id=11110379
# usage: perl create_fasta.pl > NR.fasta

use strict;
use warnings;
use List::Util 'shuffle';

# https://www.ncbi.nlm.nih.gov/nuccore/NR_165028.1?report=fasta

my $nr_partial_seq = <<'EOSEQ';
TGGCTCAGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGAGAAGGATCCTTCGGGATCTG
GAGAGCGGCGGACGGGTGAGTAACGCGTGGGAACGTGCCCTTAGGTGGGGGACAACAGTTGGAAACGACT
GCTAATACCGCATAAGCCAATTTGGGAAAGCCTTCGGGCGCCTTGGGATCGGCCCGCGTTAGATTAGGTA
GTTGGTGGGGTAAAGGCCTACCAAGCCTACGATCTATAGCTGGTTTGAGAGAATGATCAGCCACACTGGG
ACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGAC
GCAGCCATGCCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTCAACGGTGAAGATGATGACTG
TAGCCGTAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTT
CGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGACTGACCAGTCAGGGGTGAAATCCCGAGGCTCAACCT
CGGAACTGCCTTTGATACTGTCAGTCTAGAGTCTGTGAGAGGATGACGGAATACCCAGTGTAGAGGTGAA
ATTCGTAGATATTGGGTAGAACACCGGTGGCGAAGGCGGTCATCTGGCGCAGCACTGACGCTGAGGCGCG
AAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTGTGCTAGCCGTCG
GGAGTTAGGCTCTCGGTGGCGCCGCTAACGCATTAAGCACACCGCCTGGGGAGTACGGTCGCAAGATTAA
AACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGCAGA
ACCTTACCAACCCTTGACATGTGAAGTTTGGTTAGTGGAGACACTTTCCTTCAGTTCGGCTGGCTTCAAC
ACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACC
CTCACCCTTAGTTGCCATCATTTAGTTGGGCACTCTAGGGGAACTGCCGGTGACAAGCCGGAGGAAGGCG
GGGATGACGTCAAGTCCTCATGGCCCTTATGGGTTGGGCTACACACGTGCTACAATGGCGACTACAGAGG
GCAGCGAGGCGGCAACGCCAAGCAAATCCCAAAAAGTCGTCTCAGTTCGGATTGTTCTCTGCAACTCGAG
AGCATGAAGGCGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTAC
ACACCGCCCGTCACACCATGGGAGTTGGTTTTACCCGAAGACGGTGGGCTAACCGTAAGGAAGCAGCCGG
CCACGGTAAGATCAGCGACTGGGGTGAAGTC
EOSEQ

$nr_partial_seq =~ s/\s//g;

srand 42;

for ( 1..1e5 ) {
    my $nr  = sprintf('%06d', $_);
    my $seq = join '', shuffle(split //, $nr_partial_seq), "\n";

    print ">NR_${nr} Fake 16S ribosomal RNA, partial sequence\n";

    while ( $seq ) {
        my $s = substr($seq, 0, 70, '');
        print "$s\n";
    }
}

[download]

Part Two create fake peptides file

# https://www.perlmonks.org/?node_id=11110379
# usage: perl create_peptides.pl > peptides.txt

use strict;
use warnings;
use List::Util 'shuffle';

# https://www.ncbi.nlm.nih.gov/nuccore/NR_165028.1?report=fasta

my $nr_partial_seq = <<'EOSEQ';
TGGCTCAGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGAGAAGGATCCTTCGGGATCTG
GAGAGCGGCGGACGGGTGAGTAACGCGTGGGAACGTGCCCTTAGGTGGGGGACAACAGTTGGAAACGACT
GCTAATACCGCATAAGCCAATTTGGGAAAGCCTTCGGGCGCCTTGGGATCGGCCCGCGTTAGATTAGGTA
GTTGGTGGGGTAAAGGCCTACCAAGCCTACGATCTATAGCTGGTTTGAGAGAATGATCAGCCACACTGGG
ACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGAC
GCAGCCATGCCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTCAACGGTGAAGATGATGACTG
TAGCCGTAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTT
CGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGACTGACCAGTCAGGGGTGAAATCCCGAGGCTCAACCT
CGGAACTGCCTTTGATACTGTCAGTCTAGAGTCTGTGAGAGGATGACGGAATACCCAGTGTAGAGGTGAA
ATTCGTAGATATTGGGTAGAACACCGGTGGCGAAGGCGGTCATCTGGCGCAGCACTGACGCTGAGGCGCG
AAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTGTGCTAGCCGTCG
GGAGTTAGGCTCTCGGTGGCGCCGCTAACGCATTAAGCACACCGCCTGGGGAGTACGGTCGCAAGATTAA
AACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGCAGA
ACCTTACCAACCCTTGACATGTGAAGTTTGGTTAGTGGAGACACTTTCCTTCAGTTCGGCTGGCTTCAAC
ACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACC
CTCACCCTTAGTTGCCATCATTTAGTTGGGCACTCTAGGGGAACTGCCGGTGACAAGCCGGAGGAAGGCG
GGGATGACGTCAAGTCCTCATGGCCCTTATGGGTTGGGCTACACACGTGCTACAATGGCGACTACAGAGG
GCAGCGAGGCGGCAACGCCAAGCAAATCCCAAAAAGTCGTCTCAGTTCGGATTGTTCTCTGCAACTCGAG
AGCATGAAGGCGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTAC
ACACCGCCCGTCACACCATGGGAGTTGGTTTTACCCGAAGACGGTGGGCTAACCGTAAGGAAGCAGCCGG
CCACGGTAAGATCAGCGACTGGGGTGAAGTC
EOSEQ

$nr_partial_seq =~ s/\s//g;

srand 42;

my $len = length($nr_partial_seq) - 20;

for ( 1..100 ) {
    my $seq = join '', shuffle(split //, $nr_partial_seq), "\n";
    print substr($seq, rand($len), 15), "\n";
}

[download]

That covers the two input files. The usage is at the top of the script. The next post will contain the create_db and search_db scripts.

Regards, Mario

In reply to Re: Problem in RAM usage while threading the program by marioroy
in thread Problem in RAM usage while threading the program by beherasan

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