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Assembly Quick Stats #5

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Jul 26, 2018
Merged

Assembly Quick Stats #5

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7806fae
Rename assembly stats to quick
ebelter Jul 25, 2018
4343970
Assembly Stats Quick
ebelter Jul 26, 2018
5be9c51
Assembly Stats
ebelter Jul 26, 2018
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171 changes: 2 additions & 169 deletions lib/Tenx/Assembly/Command/Stats.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -3,176 +3,9 @@ package Tenx::Assembly::Command::Stats;
use strict;
use warnings 'FATAL';

use Bio::SeqIO;
use Data::Dumper;
use Path::Class;
use Text::CSV;
use YAML;

class Tenx::Assembly::Command::Stats {
is => 'Command::V2',
has_input => {
fasta_file => {
is => 'Text',
doc => 'Fasta file to derive assembly stats.',
},
},
has_optional_input => {
min_gap_size => {
is => 'Number',
default_value => 1,
doc => 'Minimum ',
},
},
has_calculated_constant_optional => {
_directory => { calculate_from => [qw/ directory /], calculate => q| Path::Class::dir($directory) |, },
summary_file => { calculate_from => [qw/ _directory /], calculate => q| $_directory->subdir('outs')->file('summary.csv') |, },
},
is => 'Command::Tree',
doc => 'stats for assemblies',
};

sub execute {
my ($self) = @_;

my $fasta_file = $self->fasta_file;
$self->fatal_message('Fasta file does not exist! %s', $fasta_file) if not -f $fasta_file or not -s $fasta_file;
my $reader = Bio::SeqIO->new(
-format => 'fasta',
-file => $fasta_file,
);

my $min_Ns_for_gap = $self->min_gap_size;
my %metrics;
my @scaf_lengths;
my @ctg_lengths;
my $max_scaffold_length = 0;
my $max_contig_length = 0;
while( my $seq = $reader->next_seq ) {
#print 'Processing '.$seq->id."\n";
my $scaffold_length = length $seq->seq;
set_breakdown_length( \%metrics, $scaffold_length, 'SCAF' );
$metrics{'SCAFFOLD_LENGTHS'} += $scaffold_length;
$metrics{'SCAFFOLD_COUNT'}++;
#push @{$metrics{'IND_SCAFFOLDS_LENGTHS'}}, $scaffold_length;
push @scaf_lengths, $scaffold_length;
if( $scaffold_length > $max_scaffold_length ) {
$metrics{'MAX_SCAFFOLD_LENGTH'} = $scaffold_length;
$max_scaffold_length = $scaffold_length;
$metrics{'MAX_SCAFFOLD_ID'} = $seq->id;
my $sequence = $seq->seq;
$sequence =~ s/N//ig;
$metrics{'MAX_SCAFFOLD_BASES_LENGTH'} = length $sequence;
}
my @contigs = split(/N{$min_Ns_for_gap,}+/i, $seq->seq);
#print Dumper \@contigs;
for my $contig( @contigs ) {
my $contig_length = length $contig;
set_breakdown_length( \%metrics, $contig_length, 'CTG' );
push @ctg_lengths, $contig_length;
$metrics{'CONTIG_LENGTHS'} += $contig_length;
$metrics{'CONTIG_COUNT'}++;
if( $contig_length > $max_contig_length ) {
$metrics{'MAX_CONTIG_LENGTH'} = $contig_length;
$max_contig_length = $contig_length;
}
}
}

#print YAML::Dump \%metrics;

# CALCULATE n50 length
@scaf_lengths = sort {$b<=>$a} @scaf_lengths;
my $n50_length = 0;
my $total_lengths;
for( 0 .. $#scaf_lengths ) {
my $length = $scaf_lengths[$_];
$total_lengths += $length;
if( $total_lengths > ( $metrics{'SCAFFOLD_LENGTHS'} * 0.5 ) ) {
$n50_length = $scaf_lengths[ $_ - 1].' ('.$scaf_lengths[$_].') '.$scaf_lengths[ $_ + 1 ];
last;
}
}

@ctg_lengths = sort {$b<=>$a} @ctg_lengths;
my $n50_ctg_length = 0;
$total_lengths = 0;
for( 0 .. $#ctg_lengths ) {
my $length = $ctg_lengths[$_];
$total_lengths += $length;
if( $total_lengths > ( $metrics{'CONTIG_LENGTHS'} * 0.5 ) ) {
$n50_ctg_length = $ctg_lengths[ $_ - 1 ].' ('.$ctg_lengths[$_].') '.$ctg_lengths[ $_ + 1 ];
last;
}
}

print "SCAFFOLDS\n";
printf( " %-10s%-15s\n", 'COUNT', $metrics{'SCAFFOLD_COUNT'} );
printf( " %-10s%-15s\n", 'LENGTH', $metrics{'SCAFFOLD_LENGTHS'} );
printf( " %-10s%-15s\n", 'AVG', int( $metrics{'SCAFFOLD_LENGTHS'} / $metrics{'SCAFFOLD_COUNT'} ) );
printf( " %-10s%-15s\n", 'N50', $n50_length);
printf( " %-10s%-15s\n", 'LARGEST', $metrics{'MAX_SCAFFOLD_LENGTH'} );
print ' (ID: '.$metrics{'MAX_SCAFFOLD_ID'}.', BASES_ONLY_LENGTH: '.$metrics{'MAX_SCAFFOLD_BASES_LENGTH'}.")\n";
print_length_bd( \%metrics, 'SCAF' );
print "\nCONTIGS\n";
printf( " %-10s%-15s\n", 'COUNT', $metrics{'CONTIG_COUNT'} );
printf( " %-10s%-15s\n", 'LENGTH', $metrics{'CONTIG_LENGTHS'} );
printf( " %-10s%-15s\n", 'AVG', int( $metrics{'CONTIG_LENGTHS'} / $metrics{'CONTIG_COUNT'} ) );
printf( " %-10s%-15s\n", 'N50', $n50_ctg_length);
printf( " %-10s%-15s\n", 'LARGEST', $metrics{'MAX_CONTIG_LENGTH'} );
print_length_bd( \%metrics, 'CTG' );
}

sub print_length_bd {
my ($metrics, $type) = @_;
my $subject = ( $type eq 'SCAF' )
? 'Scaffolds'
: 'Contigs' ;
my @len_types = ('> 1M', '250K--1M', '100K--250K', '10K--100K', '5K--10K', '2K--5K', '0--2K');
for my $len_type( @len_types ) {
my $length = ( exists $metrics->{'BD'}{$type}{$len_type}{'len'} )
? $metrics->{'BD'}{$type}{$len_type}{'len'}
: 0 ;
my $count = ( exists $metrics->{'BD'}{$type}{$len_type}{'ct'} )
? $metrics->{'BD'}{$type}{$len_type}{'ct'}
: 0 ;
print " $subject $len_type: $count ( $length bp )\n";
}
}

sub set_breakdown_length {
my ($metrics, $length, $type) = @_;
my @len_types = ('> 1M', '250K--1M', '100K--250K', '10K--100K', '5K--10K', '2K--5K', '0--2K');
if( $length > 1000000 ) {
$metrics->{'BD'}{$type}{$len_types[0]}{'len'} += $length;
$metrics->{'BD'}{$type}{$len_types[0]}{'ct'} ++;
}
elsif( $length > 250000 ) {
$metrics->{'BD'}{$type}{$len_types[1]}{'len'} += $length;
$metrics->{'BD'}{$type}{$len_types[1]}{'ct'} ++;
}
elsif( $length > 100000 ) {
$metrics->{'BD'}{$type}{$len_types[2]}{'len'} += $length;
$metrics->{'BD'}{$type}{$len_types[2]}{'ct'} ++;
}
elsif( $length > 10000 ) {
$metrics->{'BD'}{$type}{$len_types[3]}{'len'} += $length;
$metrics->{'BD'}{$type}{$len_types[3]}{'ct'} ++;
}
elsif( $length > 5000 ) {
$metrics->{'BD'}{$type}{$len_types[4]}{'len'} += $length;
$metrics->{'BD'}{$type}{$len_types[4]}{'ct'} ++;
}
elsif( $length > 2000 ) {
$metrics->{'BD'}{$type}{$len_types[5]}{'len'} += $length;
$metrics->{'BD'}{$type}{$len_types[5]}{'ct'} ++;
}
elsif( $length > 0 ) {
$metrics->{'BD'}{$type}{$len_types[6]}{'len'} += $length;
$metrics->{'BD'}{$type}{$len_types[6]}{'ct'} ++;
}
else {
# shouldn't happen
die "TYPE: $type, LENGHT: $length\n";
}
}

1;
162 changes: 162 additions & 0 deletions lib/Tenx/Assembly/Command/Stats/Quick.pm
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@@ -0,0 +1,162 @@
package Tenx::Assembly::Command::Stats::Quick;

use strict;
use warnings 'FATAL';

use Bio::SeqIO;
use List::Util;

class Tenx::Assembly::Command::Stats::Quick {
is => 'Command::V2',
has_input => {
fasta_file => {
is => 'Text',
doc => 'Fasta file to derive assembly stats.',
},
},
has_optional_input => {
min_gap_size => {
is => 'Number',
default_value => 1,
doc => 'Minimum ',
},
},
};

sub execute {
my ($self) = @_;

my $fasta_file = $self->fasta_file;
$self->fatal_message('Fasta file does not exist! %s', $fasta_file) if not -f $fasta_file or not -s $fasta_file;
my $reader = Bio::SeqIO->new(
-format => 'fasta',
-file => $fasta_file,
);

my $min_Ns_for_gap = $self->min_gap_size;
my %metrics;
my @scaf_lengths;
my @ctg_lengths;
my $max_scaffold_length = -1;
my $max_contig_length = -1;
while( my $seq = $reader->next_seq ) {
my $sequence = $seq->seq || '';
my $scaffold_length = $seq->length || 0;
my $bd_length = get_breakdown_length($scaffold_length);
$metrics{'BD'}{'SCAF'}{$bd_length}{'len'} += $scaffold_length;
$metrics{'BD'}{'SCAF'}{$bd_length}{'ct'}++;
$metrics{'SCAFFOLD_LENGTHS'} += $scaffold_length;
$metrics{'SCAFFOLD_COUNT'}++;
push @scaf_lengths, $scaffold_length;
if( $scaffold_length > $max_scaffold_length ) {
$metrics{'MAX_SCAFFOLD_LENGTH'} = $scaffold_length;
$max_scaffold_length = $scaffold_length;
$metrics{'MAX_SCAFFOLD_ID'} = $seq->id;
$sequence =~ s/N//ig;
$metrics{'MAX_SCAFFOLD_BASES_LENGTH'} = length $sequence;
}
my @contigs = ( $scaffold_length > 0 )
? split( /N{$min_Ns_for_gap,}+/i, ($sequence || '') )
: '';
#my @contigs = split( /N{$min_Ns_for_gap,}+/i, ($seq->seq || '') );
for my $contig( @contigs ) {
my $contig_length = length $contig;
my $bd_length = get_breakdown_length($contig_length);
$metrics{'BD'}{'CTG'}{$bd_length}{'len'} += $contig_length;
$metrics{'BD'}{'CTG'}{$bd_length}{'ct'}++;
push @ctg_lengths, $contig_length;
$metrics{'CONTIG_LENGTHS'} += $contig_length;
$metrics{'CONTIG_COUNT'}++;
if( $contig_length > $max_contig_length ) {
$metrics{'MAX_CONTIG_LENGTH'} = $contig_length;
$max_contig_length = $contig_length;
}
}
}

@scaf_lengths = sort {$b<=>$a} @scaf_lengths;
my $n50_length = 0;
my $total_lengths;
for( 0 .. $#scaf_lengths ) {
my $length = $scaf_lengths[$_];
$total_lengths += $length;
if( $total_lengths > ( $metrics{'SCAFFOLD_LENGTHS'} * 0.5 ) ) {
$n50_length = $scaf_lengths[ $_ - 1].' ('.$scaf_lengths[$_].') '.$scaf_lengths[ $_ + 1 ];
last;
}
}

@ctg_lengths = sort {$b<=>$a} @ctg_lengths;
my $n50_ctg_length = 0;
$total_lengths = 0;
for( 0 .. $#ctg_lengths ) {
my $length = $ctg_lengths[$_];
$total_lengths += $length;
if( $total_lengths > ( $metrics{'CONTIG_LENGTHS'} * 0.5 ) ) {
$n50_ctg_length = $ctg_lengths[ $_ - 1 ].' ('.$ctg_lengths[$_].') '.$ctg_lengths[ $_ + 1 ];
last;
}
}

print "SCAFFOLDS\n";
printf( " %-10s%-15s\n", 'COUNT', $metrics{'SCAFFOLD_COUNT'} );
printf( " %-10s%-15s\n", 'LENGTH', $metrics{'SCAFFOLD_LENGTHS'} );
printf( " %-10s%-15s\n", 'AVG', int( $metrics{'SCAFFOLD_LENGTHS'} / $metrics{'SCAFFOLD_COUNT'} ) );
printf( " %-10s%-15s\n", 'N50', $n50_length);
printf( " %-10s%-15s\n", 'LARGEST', $metrics{'MAX_SCAFFOLD_LENGTH'} );
print ' (ID: '.$metrics{'MAX_SCAFFOLD_ID'}.', BASES_ONLY_LENGTH: '.$metrics{'MAX_SCAFFOLD_BASES_LENGTH'}.")\n";
print_length_bd( \%metrics, 'SCAF' );
print "\nCONTIGS\n";
printf( " %-10s%-15s\n", 'COUNT', $metrics{'CONTIG_COUNT'} );
printf( " %-10s%-15s\n", 'LENGTH', $metrics{'CONTIG_LENGTHS'} );
printf( " %-10s%-15s\n", 'AVG', int( $metrics{'CONTIG_LENGTHS'} / $metrics{'CONTIG_COUNT'} ) );
printf( " %-10s%-15s\n", 'N50', $n50_ctg_length);
printf( " %-10s%-15s\n", 'LARGEST', $metrics{'MAX_CONTIG_LENGTH'} );
print_length_bd( \%metrics, 'CTG' );
}

sub lengths_and_labels {
{
1000000 => '> 1M',
250000 => '250K--1M',
100000 => '100K--250K',
10000 => '10K--100K',
5000 => '5K--10K',
2000 => '2K--5K',
0 => '0--2K',
}
}
sub bd_lengths {
my $lengths_and_labels = lengths_and_labels();
sort { $b <=> $a } keys %$lengths_and_labels;
}
sub get_label_for_bd_length {
my ($bd_length) = @_;
die "No bd_length given to get_label_for_bd_length!" if not defined $bd_length;
my $lengths_and_labels = lengths_and_labels();
$lengths_and_labels->{$bd_length};
}

sub print_length_bd {
my ($metrics, $type) = @_;
my $subject = ( $type eq 'SCAF' )
? 'Scaffolds'
: 'Contigs' ;
for my $bd_length ( bd_lengths() ) {
my $length = ( exists $metrics->{'BD'}{$type}{$bd_length}{'len'} )
? $metrics->{'BD'}{$type}{$bd_length}{'len'}
: 0 ;
my $count = ( exists $metrics->{'BD'}{$type}{$bd_length}{'ct'} )
? $metrics->{'BD'}{$type}{$bd_length}{'ct'}
: 0 ;
printf(" $subject %s: $count ( $length bp )\n", get_label_for_bd_length($bd_length));
}
}

sub get_breakdown_length {
my ($length) = @_;
die "No length given to get_breakdown_length" if not defined $length;
List::Util::first { $length >= $_ } bd_lengths();
}

1;
57 changes: 57 additions & 0 deletions t/Tenx-Assembly-Command-Stats-Quick.t
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@@ -0,0 +1,57 @@
#!/usr/bin/env perl

use strict;
use warnings 'FATAL';

use TenxTestEnv;

use File::Slurp 'slurp';
use Test::Exception;
use Test::More tests => 4;

my %test;
subtest 'setup' => sub{
plan tests => 2;

$test{class} = 'Tenx::Assembly::Command::Stats::Quick';
use_ok($test{class}) or die;
$test{data_dir} = TenxTestEnv::test_data_directory_for_class($test{class});
ok(-d $test{data_dir}, 'data dir exists');


};

subtest 'success' => sub{
plan tests => 3;

my $output;
open local(*STDOUT), '>', \$output or die $!;
lives_ok(sub{ $test{class}->execute(fasta_file => $test{data_dir}->file('fasta')->stringify); }, 'execute');

my $expected_output = slurp($test{data_dir}->file('fasta.stats')->stringify);
ok($expected_output, 'loaded expected output');
is($output, $expected_output, 'output matches');

};

subtest 'success zero length scaffold' => sub{
plan tests => 3;

my $output;
open local(*STDOUT), '>', \$output or die $!;
lives_ok(sub{ $test{class}->execute(fasta_file => $test{data_dir}->file('zero-length-scaffold.fasta')->stringify); }, 'execute');

my $expected_output = slurp($test{data_dir}->file('zero-length-scaffold.fasta.stats')->stringify);
ok($expected_output, 'loaded expected output');
is($output, $expected_output, 'output matches');

};

subtest 'fails' => sub{
plan tests => 1;

throws_ok(sub{ $test{class}->execute(fasta_file => $test{data_dir}->stringify); }, qr/Fasta file does not exist/, 'execute fails w/ non existing fasta file');

};

done_testing();
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