Bio_AssemblyImprovement
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bin/fill_gaps_with_gapfiller view on Meta::CPAN
=head1 NAME
fill_gaps_with_gapfiller - Given an assembly iteratively fill gaps
=head1 VERSION
version 1.160490
=head1 SYNOPSIS
Given an assembly and some reads in fastq format, try and fill in the gaps. Do multiple iterations with different values, and cleanup all intermediate files.
# outputs a file called contigs.scaffolded.fa
fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq
# use two threads (default 1)
fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq -t 2
# Gzipped input files are accepted
fill_gaps_with_gapfiller -a contigs.fa.gz -f 123_1.fastq.gz -r 123_2.fastq.gz
bin/scaffold_with_sspace view on Meta::CPAN
=head1 NAME
scaffold_with_sspace - Given an assembly and some reads in fastq format, try and scaffold the assembly.
=head1 VERSION
version 1.160490
=head1 SYNOPSIS
Given an assembly and some reads in fastq format, try and scaffold the assembly. Do multiple iterations with different values, and cleanup all intermediate files.
# outputs a file called contigs.scaffolded.fa
scaffold_with_sspace -a contigs.fa -f 123_1.fastq -r 123_2.fastq
# use two threads (default 1)
scaffold_with_sspace -a contigs.fa -f 123_1.fastq -r 123_2.fastq -t 2
# Gzipped input files are accepted
scaffold_with_sspace -a contigs.fa.gz -f 123_1.fastq.gz -r 123_2.fastq.gz
lib/Bio/AssemblyImprovement/Circlator/Main.pm view on Meta::CPAN
if(! -d $self->output_directory){
make_path($self->output_directory);
}
system("mv $temp_dir/00.info.txt ".$self->output_directory."/circlator.info.txt") and warn "Could not move $temp_dir/00.info.txt to ".$self->output_directory."/circlator.info.txt";
system("mv $temp_dir/06.fixstart.fasta ".$self->output_directory."/circlator.final.fasta") and die "Could not move $temp_dir/06.fixstart.fasta to ".$self->output_directory."/circlator.final.fasta";
my @iterative_merge_files = sort {$self->_get_number_in_filename($a) <=> $self->_get_number_in_filename($b)} glob("$temp_dir/04.merge.merge.iter.*.reads.log"); #cannot rely on glob's lexical sorting
my @log_files = ("$temp_dir/02.bam2reads.log",
@iterative_merge_files,
"$temp_dir/04.merge.merge.iterations.log",
"$temp_dir/04.merge.merge.log",
"$temp_dir/04.merge.circularise_details.log",
"$temp_dir/04.merge.circularise.log",
"$temp_dir/05.clean.log",
"$temp_dir/06.fixstart.log",
);
my $filtered_log_files = $self->_filter_out_non_existant_files(\@log_files);
system("cat ".join(" ", @{$filtered_log_files})." > ".$self->output_directory."/circlator.log") and warn "Could not cat circlator log files to ".$self->output_directory."/circlator.log";
remove_tree($temp_dir) if(-d $temp_dir);
lib/Bio/AssemblyImprovement/FillGaps/GapFiller/Main.pm view on Meta::CPAN
with 'Bio::AssemblyImprovement::Scaffold::SSpace::OutputFilenameRole';
with 'Bio::AssemblyImprovement::Scaffold::SSpace::TempDirectoryRole';
has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'insert_size' => ( is => 'ro', isa => 'Int', required => 1 );
has 'mapper' => ( is => 'ro', isa => 'Str', default => 'bwa' );
has 'merge_size' => ( is => 'ro', isa => 'Int', default => 10 );
has 'threads' => ( is => 'ro', isa => 'Int', default => 1 );
has 'gap_filler_exec' => ( is => 'rw', isa => 'Str', required => 1 );
has 'debug' => ( is => 'ro', isa => 'Bool', default => 0 );
has 'num_iterations' => ( is => 'ro', isa => 'Int', default => 20 );
has '_config_file_obj' => ( is => 'ro', isa => 'Bio::AssemblyImprovement::FillGaps::GapFiller::Config', lazy => 1, builder => '_build__config_file_obj' );
sub _build__config_file_obj {
my ($self) = @_;
Bio::AssemblyImprovement::FillGaps::GapFiller::Config->new(
input_files => $self->input_files,
insert_size => $self->insert_size,
output_filename => join( '/', ( $self->_temp_directory, '_gap_filler.config' ) ),
mapper => $self->mapper
lib/Bio/AssemblyImprovement/FillGaps/GapFiller/Main.pm view on Meta::CPAN
my $stdout_of_program = '';
$stdout_of_program = "> /dev/null 2>&1" if($self->debug == 0);
system(
join(
' ',
(
'perl', $self->gap_filler_exec,
'-l', $self->_config_file_obj->output_filename,
'-s', $self->input_assembly,
'-i', $self->num_iterations,
'-m', $self->merge_size,
'-T', $self->threads,
'-b', $self->_output_prefix,
$stdout_of_program
)
)
);
move( $self->_intermediate_file_name, $self->output_filename );
chdir($original_cwd);
return $self;
lib/Bio/AssemblyImprovement/Scaffold/SSpace/Iterative.pm view on Meta::CPAN
input_assembly => 'contigs.fa'
insert_size => 250,
scaffolder_exec => '/path/to/SSPACE.pl',
merge_sizes => [100,50,30,10]
)->run;
=head1 METHODS
=head2 run
Run the iterations of SSpace
=head1 SEE ALSO
=for :list * L<Bio::AssemblyImprovement::Scaffold::SSpace::Config>
* L<Bio::AssemblyImprovement::Scaffold::SSpace::Main>
=head1 AUTHOR
Andrew J. Page <ap13@sanger.ac.uk>
t/dummy_circlator_script view on Meta::CPAN
my @circlator_output_files = ("00.info.txt",
"00.input_assembly.fasta",
"00.input_assembly.fasta.fai",
"01.mapreads.bam",
"01.mapreads.bam.bai",
"02.bam2reads.log",
"02.bam2reads.fasta",
"04.merge.coords",
"04.merge.fasta",
"04.merge.merge.iterations.log",
"04.merge.merge.log",
"04.merge.circularise_details.log",
"04.merge.circularise.log",
"04.merge.merge.iter.1.reads.log",
"04.merge.merge.iter.2.reads.log",
"04.merge.merge.iter.10.reads.log",
"05.clean.contigs_to_keep",
"05.clean.log",
"05.clean.coords",
"05.clean.fasta",
t/dummy_circlator_script view on Meta::CPAN
system("mkdir $dir");
chdir ("$dir");
system("touch ".join(" ", @circlator_output_files));
system("mkdir ".join(" ", @circlator_output_dir));
# test logs
system("echo log_1 > 02.bam2reads.log");
system("echo log_2 > 04.merge.merge.iter.1.reads.log");
system("echo log_3 > 04.merge.merge.iter.2.reads.log");
system("echo log_4 > 04.merge.merge.iter.10.reads.log");
system("echo log_5 > 04.merge.merge.iterations.log");
system("echo log_6 > 04.merge.merge.log");
system("echo log_7 > 04.merge.circularise_details.log");
system("echo log_8 > 04.merge.circularise.log");
system("echo log_9 > 05.clean.log");
system("echo log_10 > 06.fixstart.log");
chdir $cwd;
t/dummy_circlator_script_no_merge_log view on Meta::CPAN
my @circlator_output_files = ("00.info.txt",
"00.input_assembly.fasta",
"00.input_assembly.fasta.fai",
"01.mapreads.bam",
"01.mapreads.bam.bai",
"02.bam2reads.log",
"02.bam2reads.fasta",
"04.merge.coords",
"04.merge.fasta",
"04.merge.merge.iterations.log",
"04.merge.circularise_details.log",
"04.merge.circularise.log",
"04.merge.merge.iter.1.reads.log",
"04.merge.merge.iter.2.reads.log",
"04.merge.merge.iter.10.reads.log",
"05.clean.contigs_to_keep",
"05.clean.log",
"05.clean.coords",
"05.clean.fasta",
"05.clean.remove_small.fa",
t/dummy_circlator_script_no_merge_log view on Meta::CPAN
system("mkdir $dir");
chdir ("$dir");
system("touch ".join(" ", @circlator_output_files));
system("mkdir ".join(" ", @circlator_output_dir));
# test logs
system("echo log_1 > 02.bam2reads.log");
system("echo log_2 > 04.merge.merge.iter.1.reads.log");
system("echo log_3 > 04.merge.merge.iter.2.reads.log");
system("echo log_4 > 04.merge.merge.iter.10.reads.log");
system("echo log_5 > 04.merge.merge.iterations.log");
system("echo log_7 > 04.merge.circularise_details.log");
system("echo log_8 > 04.merge.circularise.log");
system("echo log_9 > 05.clean.log");
system("echo log_10 > 06.fixstart.log");
chdir $cwd;
( run in 1.610 second using v1.01-cache-2.11-cpan-96521ef73a4 )