comment on

It sounds like your input is in FASTQ format...? So the optimum algorithm should pass through the data ideally once.

Chopping from the back of each sequence in a single pass seems like a quick way as opposed to for example putting the sequence more than once through tr or some other regex processor.

I am not sure what your target performance is, but I picked up an example fastq file of just over 78MB and put it through this simple piece of code that uses one pass chopping. The fourteen seconds (on my 3.5GHz PC) suggest that 1 gygabyte would take about three minutes; note that the array of hash does NOT grow as more sequences are processed, so the prediction is scaleable.

#!/usr/bin/perl

use strict;
use warnings;

use Data::Dumper;
my ($file) = glob '*.fastq';

open $fh, $file;

my $analysis = []; # each element a sequence position
           # at which we will put a hash of freqs
print localtime() . "\n";
while ( my $hdr = <$fh>) {
    my $seq = <$fh>;
    chomp $seq;
    analyse($seq, $analysis);
    $seq = <$fh> for (0 .. 1); # discard trailer
}
print localtime() . "\n";
print Dumper($analysis);

sub analyse {
    my ($seq, $analysis) = @_;
    my $pos = length($seq);
    while ($pos) {
    $analysis->[--$pos]{chop $seq}++;
    }
}
[download]

which gave the following output:

Wed Jun  8 14:19:04 2016
Wed Jun  8 14:19:18 2016
$VAR1 = [
          {
            'A' => 95617,
            'T' => 108158,
            'G' => 40710,
            'C' => 64361
          },
          {
            'T' => 75373,
            'C' => 51943,
            'G' => 72545,
            'A' => 108985
          },
          {
            'T' => 85539,
            'C' => 57343,
            'G' => 69604,
            'A' => 96360
          },
          {
            'A' => 92923,
            'C' => 64361,
            'T' => 87445,
            'G' => 64117
          },
          {
            'T' => 93456,
            'G' => 60673,
            'C' => 60057,
            'A' => 94660
          },
          {
            'A' => 94775,
            'C' => 62953,
            'G' => 63212,
            'T' => 87906
          },
          {
            'A' => 92453,
            'G' => 64227,
            'C' => 60365,
            'T' => 91801
          },
          {
            'C' => 60513,
            'T' => 91077,
            'G' => 61364,
            'A' => 95892
          },
          {
            'C' => 60524,
            'G' => 60844,
            'T' => 92885,
            'A' => 94593
          },
          {
            'A' => 94766,
            'G' => 61648,
            'C' => 60955,
            'T' => 91477
          },
          {
            'T' => 92978,
            'G' => 60935,
            'C' => 60316,
            'A' => 94617
          },
          {
            'C' => 60539,
            'G' => 61581,
            'T' => 92274,
            'A' => 94452
          },
          {
            'C' => 59940,
            'G' => 60190,
            'T' => 93538,
            'A' => 95178
          },
          {
            'G' => 60608,
            'C' => 60446,
            'T' => 93249,
            'A' => 94543
          },
          {
            'A' => 94666,
            'T' => 93556,
            'C' => 59989,
            'G' => 60635
          },
          {
            'C' => 60324,
            'G' => 61720,
            'T' => 93268,
            'A' => 93534
          },
          {
            'A' => 93717,
            'C' => 60376,
            'T' => 93535,
            'G' => 61218
          },
          {
            'G' => 61225,
            'C' => 60992,
            'T' => 93130,
            'A' => 93499
          },
          {
            'A' => 93515,
            'C' => 61161,
            'G' => 61151,
            'T' => 93019
          },
          {
            'A' => 92598,
            'C' => 61351,
            'T' => 93131,
            'G' => 61766
          },
          {
            'A' => 93152,
            'C' => 61278,
            'T' => 92889,
            'G' => 61527
          },
          {
            'A' => 93143,
            'C' => 61225,
            'G' => 62000,
            'T' => 92478
          },
          {
            'G' => 61474,
            'T' => 92977,
            'C' => 61546,
            'A' => 92849
          },
          {
            'A' => 92661,
            'G' => 61980,
            'C' => 61768,
            'T' => 92437
          },
          {
            'G' => 62070,
            'C' => 61778,
            'T' => 92189,
            'A' => 92809
          },
          {
            'A' => 92502,
            'T' => 92386,
            'C' => 61611,
            'G' => 62347
          },
          {
            'A' => 92432,
            'T' => 91737,
            'G' => 62648,
            'C' => 62029
          },
          {
            'T' => 91679,
            'G' => 62252,
            'C' => 62089,
            'A' => 92826
          },
          {
            'G' => 62453,
            'T' => 91892,
            'C' => 61765,
            'A' => 92736
          },
          {
            'G' => 62708,
            'T' => 92085,
            'C' => 61591,
            'A' => 92462
          },
          {
            'C' => 62291,
            'T' => 91884,
            'G' => 62821,
            'A' => 91850
          },
          {
            'G' => 62700,
            'T' => 91738,
            'C' => 62320,
            'A' => 92088
          },
          {
            'A' => 93030,
            'C' => 61746,
            'G' => 62788,
            'T' => 91282
          },
          {
            'T' => 91749,
            'C' => 61744,
            'G' => 62907,
            'A' => 92446
          },
          {
            'G' => 62296,
            'T' => 91632,
            'C' => 62216,
            'A' => 92702
          },
          {
            'T' => 91804,
            'C' => 62383,
            'G' => 62855,
            'N' => 1,
            'A' => 91803
          },
          {
            'C' => 61646,
            'G' => 62903,
            'T' => 91341,
            'A' => 92667,
            'N' => 289
          },
          {
            'C' => 62641,
            'G' => 62872,
            'T' => 91136,
            'A' => 92197
          },
          {
            'C' => 62057,
            'G' => 62837,
            'T' => 91154,
            'N' => 620,
            'A' => 92178
          },
          {
            'G' => 62722,
            'C' => 62043,
            'T' => 91622,
            'N' => 576,
            'A' => 91883
          },
          {
            'C' => 61811,
            'T' => 91391,
            'G' => 63307,
            'A' => 92337
          },
          {
            'A' => 91767,
            'N' => 620,
            'C' => 62239,
            'G' => 63172,
            'T' => 91048
          },
          {
            'A' => 91871,
            'N' => 53,
            'G' => 63084,
            'C' => 62200,
            'T' => 91638
          },
          {
            'T' => 91688,
            'G' => 62924,
            'C' => 61981,
            'N' => 385,
            'A' => 91868
          },
          {
            'G' => 63108,
            'C' => 62768,
            'T' => 91005,
            'N' => 419,
            'A' => 91546
          },
          {
            'A' => 91701,
            'N' => 621,
            'C' => 62578,
            'G' => 63091,
            'T' => 90855
          },
          {
            'A' => 91816,
            'N' => 71,
            'C' => 62275,
            'T' => 91096,
            'G' => 63588
          },
          {
            'A' => 91525,
            'N' => 236,
            'C' => 62607,
            'T' => 91383,
            'G' => 63095
          },
          {
            'A' => 91080,
            'N' => 26,
            'G' => 63213,
            'T' => 91594,
            'C' => 62933
          },
          {
            'A' => 91514,
            'N' => 51,
            'T' => 91087,
            'G' => 63341,
            'C' => 62853
          },
          {
            'G' => 63314,
            'C' => 62538,
            'T' => 90800,
            'N' => 593,
            'A' => 91601
          },
          {
            'G' => 63782,
            'T' => 90949,
            'C' => 62223,
            'N' => 807,
            'A' => 91085
          },
          {
            'N' => 620,
            'A' => 91394,
            'T' => 90938,
            'C' => 62302,
            'G' => 63592
          },
          {
            'A' => 91299,
            'N' => 605,
            'G' => 63677,
            'C' => 62200,
            'T' => 91065
          },
          {
            'A' => 91432,
            'N' => 622,
            'G' => 63535,
            'C' => 62496,
            'T' => 90761
          },
          {
            'G' => 63791,
            'T' => 90401,
            'C' => 62571,
            'N' => 625,
            'A' => 91458
          },
          {
            'G' => 63397,
            'C' => 62282,
            'T' => 90597,
            'A' => 91847,
            'N' => 723
          },
          {
            'C' => 62021,
            'G' => 63202,
            'T' => 91192,
            'A' => 92137,
            'N' => 294
          },
          {
            'T' => 90904,
            'G' => 63432,
            'C' => 62605,
            'A' => 91411,
            'N' => 494
          },
          {
            'A' => 91268,
            'N' => 294,
            'T' => 90559,
            'C' => 63196,
            'G' => 63529
          },
          {
            'T' => 90368,
            'G' => 63510,
            'C' => 62999,
            'N' => 371,
            'A' => 91598
          },
          {
            'A' => 91073,
            'N' => 713,
            'T' => 90533,
            'C' => 62880,
            'G' => 63647
          },
          {
            'G' => 63387,
            'C' => 62393,
            'T' => 91009,
            'N' => 729,
            'A' => 91328
          },
          {
            'C' => 62732,
            'G' => 63781,
            'T' => 90418,
            'N' => 373,
            'A' => 91542
          },
          {
            'C' => 62653,
            'T' => 90784,
            'G' => 63484,
            'N' => 290,
            'A' => 91635
          },
          {
            'N' => 140,
            'A' => 91372,
            'G' => 64039,
            'T' => 90277,
            'C' => 63018
          },
          {
            'C' => 63377,
            'T' => 90129,
            'G' => 63458,
            'A' => 91258,
            'N' => 624
          },
          {
            'T' => 90870,
            'G' => 63823,
            'C' => 62831,
            'A' => 90667,
            'N' => 655
          },
          {
            'A' => 91640,
            'N' => 428,
            'G' => 63513,
            'T' => 90278,
            'C' => 62987
          },
          {
            'A' => 90783,
            'N' => 1166,
            'C' => 62632,
            'G' => 63972,
            'T' => 90293
          },
          {
            'A' => 91091,
            'N' => 1004,
            'G' => 64306,
            'C' => 62924,
            'T' => 89521
          },
          {
            'A' => 90956,
            'N' => 806,
            'G' => 64238,
            'T' => 89778,
            'C' => 63068
          },
          {
            'T' => 90931,
            'G' => 64216,
            'C' => 62586,
            'A' => 90584,
            'N' => 529
          },
          {
            'C' => 62968,
            'G' => 64399,
            'T' => 89490,
            'A' => 91272,
            'N' => 717
          },
          {
            'N' => 449,
            'A' => 90544,
            'G' => 64163,
            'T' => 90620,
            'C' => 63070
          },
          {
            'A' => 90839,
            'N' => 636,
            'C' => 63188,
            'G' => 64298,
            'T' => 89885
          },
          {
            'A' => 91013,
            'N' => 932,
            'G' => 63479,
            'C' => 63121,
            'T' => 90301
          },
          {
            'T' => 89829,
            'C' => 63165,
            'G' => 64210,
            'A' => 91346,
            'N' => 296
          },
          {
            'G' => 64529,
            'C' => 62714,
            'T' => 89936,
            'A' => 91477,
            'N' => 190
          },
          {
            'N' => 301,
            'A' => 90623,
            'G' => 64859,
            'C' => 63122,
            'T' => 89941
          },
          {
            'T' => 90099,
            'C' => 63211,
            'G' => 64084,
            'N' => 131,
            'A' => 91321
          },
          {
            'N' => 1475,
            'A' => 90609,
            'G' => 63896,
            'C' => 63063,
            'T' => 89803
          },
          {
            'N' => 1407,
            'A' => 91461,
            'T' => 88953,
            'G' => 64306,
            'C' => 62719
          },
          {
            'T' => 89127,
            'G' => 64231,
            'C' => 62298,
            'N' => 2177,
            'A' => 91013
          },
          {
            'A' => 90259,
            'N' => 2131,
            'C' => 62896,
            'G' => 64105,
            'T' => 89455
          },
          {
            'C' => 63197,
            'G' => 64079,
            'T' => 89832,
            'N' => 908,
            'A' => 90830
          },
          {
            'G' => 64777,
            'T' => 89976,
            'C' => 63068,
            'N' => 357,
            'A' => 90668
          },
          {
            'T' => 89587,
            'C' => 63200,
            'G' => 64812,
            'A' => 89978,
            'N' => 1269
          },
          {
            'N' => 1696,
            'A' => 89904,
            'G' => 64443,
            'C' => 63402,
            'T' => 89401
          },
          {
            'A' => 89654,
            'N' => 2703,
            'C' => 63119,
            'T' => 88903,
            'G' => 64467
          },
          {
            'N' => 1131,
            'A' => 89889,
            'T' => 89520,
            'C' => 63477,
            'G' => 64829
          },
          {
            'G' => 64882,
            'T' => 89466,
            'C' => 63907,
            'N' => 1347,
            'A' => 89244
          },
          {
            'C' => 63887,
            'G' => 64353,
            'T' => 89136,
            'A' => 90096,
            'N' => 1374
          },
          {
            'G' => 65209,
            'T' => 88684,
            'C' => 63699,
            'A' => 90123,
            'N' => 1131
          },
          {
            'C' => 63361,
            'G' => 64956,
            'T' => 89134,
            'N' => 844,
            'A' => 90551
          },
          {
            'C' => 63860,
            'T' => 88496,
            'G' => 65164,
            'A' => 89328,
            'N' => 1998
          },
          {
            'G' => 64476,
            'C' => 63725,
            'T' => 88534,
            'N' => 1816,
            'A' => 90295
          },
          {
            'C' => 63638,
            'T' => 88409,
            'G' => 64782,
            'N' => 1982,
            'A' => 90035
          },
          {
            'N' => 1594,
            'A' => 89806,
            'C' => 64095,
            'T' => 88343,
            'G' => 65008
          },
          {
            'N' => 1572,
            'A' => 89668,
            'G' => 65516,
            'C' => 63817,
            'T' => 88273
          }
        ];
[download]

One world, one people

In reply to Re: Weighted frequency of characters in an array of strings by anonymized user 468275
in thread Weighted frequency of characters in an array of strings by K_Edw

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