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Accept genbank files #121

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merged 8 commits into from
May 14, 2015
Merged

Accept genbank files #121

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3281fa6
Citation
andrewjpage May 14, 2015
6bae8b0
use proper logging and perl tidy
andrewjpage May 14, 2015
e87c238
use logging in the job runner
andrewjpage May 14, 2015
acee7e5
Extract proteins from GFF converted from GenBank format
andrewjpage May 14, 2015
e5a26e4
Set logging level
andrewjpage May 14, 2015
8eff7ff
Get rid of sanger specific path in Rscript
andrewjpage May 14, 2015
6d278a7
allow rRNA tags
andrewjpage May 14, 2015
a3c0e96
Allow for GFFs created from genbank gbff files
andrewjpage May 14, 2015
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2 changes: 1 addition & 1 deletion bin/create_pan_genome_plots.R
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/software/pathogen/external/apps/usr/local/bin/Rscript
#!/usr/bin/env Rscript
# ABSTRACT: Create R plots
# PODNAME: create_plots.R

Expand Down
2 changes: 1 addition & 1 deletion dist.ini
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
name = Bio-Roary
version = 2.1.2
version = 2.2.0
author = Andrew J. Page <ap13@sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
Expand Down
11 changes: 11 additions & 0 deletions lib/Bio/Roary/CommandLine/Common.pm
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Expand Up @@ -11,6 +11,17 @@ Common command line settings

use Moose;
use FindBin;
use Log::Log4perl qw(:easy);

has 'logger' => ( is => 'ro', lazy => 1, builder => '_build_logger');

sub _build_logger
{
my ($self) = @_;
Log::Log4perl->easy_init(level => $ERROR);
my $logger = get_logger();
return $logger;
}


sub run {
Expand Down
193 changes: 100 additions & 93 deletions lib/Bio/Roary/CommandLine/Roary.pm
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Expand Up @@ -13,41 +13,47 @@ use Getopt::Long qw(GetOptionsFromArray);
use Bio::Roary;
use Bio::Roary::PrepareInputFiles;
use Bio::Roary::QC::Report;
use File::Which;
use File::Which;
extends 'Bio::Roary::CommandLine::Common';

has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'help' => ( is => 'rw', isa => 'Bool', default => 0 );

has 'fasta_files' => ( is => 'rw', isa => 'ArrayRef' );
has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' );
has 'job_runner' => ( is => 'rw', isa => 'Str', default => 'Local' );
has 'makeblastdb_exec' => ( is => 'rw', isa => 'Str', default => 'makeblastdb' );
has 'blastp_exec' => ( is => 'rw', isa => 'Str', default => 'blastp' );
has 'mcxdeblast_exec' => ( is => 'rw', isa => 'Str', default => 'mcxdeblast' );
has 'mcl_exec' => ( is => 'rw', isa => 'Str', default => 'mcl' );
has 'apply_unknowns_filter' => ( is => 'rw', isa => 'Bool', default => 1 );
has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 );
has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'perc_identity' => ( is => 'rw', isa => 'Num', default => 98 );
has 'dont_delete_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 1 );
has 'dont_run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_split_groups' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'verbose_stats' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'translation_table' => ( is => 'rw', isa => 'Int', default => 11 );
has 'group_limit' => ( is => 'rw', isa => 'Num', default => 50000 );
has 'core_definition' => ( is => 'rw', isa => 'Num', default => 1 );
has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );

has '_error_message' => ( is => 'rw', isa => 'Str' );
has 'run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'help' => ( is => 'rw', isa => 'Bool', default => 0 );

has 'fasta_files' => ( is => 'rw', isa => 'ArrayRef' );
has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' );
has 'job_runner' => ( is => 'rw', isa => 'Str', default => 'Local' );
has 'makeblastdb_exec' => ( is => 'rw', isa => 'Str', default => 'makeblastdb' );
has 'blastp_exec' => ( is => 'rw', isa => 'Str', default => 'blastp' );
has 'mcxdeblast_exec' => ( is => 'rw', isa => 'Str', default => 'mcxdeblast' );
has 'mcl_exec' => ( is => 'rw', isa => 'Str', default => 'mcl' );
has 'apply_unknowns_filter' => ( is => 'rw', isa => 'Bool', default => 1 );
has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 );
has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'perc_identity' => ( is => 'rw', isa => 'Num', default => 98 );
has 'dont_delete_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 1 );
has 'dont_run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_split_groups' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'verbose_stats' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'translation_table' => ( is => 'rw', isa => 'Int', default => 11 );
has 'group_limit' => ( is => 'rw', isa => 'Num', default => 50000 );
has 'core_definition' => ( is => 'rw', isa => 'Num', default => 1 );
has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );

has '_error_message' => ( is => 'rw', isa => 'Str' );
has 'run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );

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

my ( $fasta_files,$verbose, $create_rplots,$group_limit, $dont_run_qc, $max_threads, $dont_delete_files, $dont_split_groups, $perc_identity, $output_filename, $job_runner, $makeblastdb_exec,$mcxdeblast_exec,$mcl_exec, $blastp_exec, $apply_unknowns_filter, $cpus,$output_multifasta_files, $verbose_stats, $translation_table, $run_qc, $core_definition, $help );
my (
$fasta_files, $verbose, $create_rplots, $group_limit, $dont_run_qc,
$max_threads, $dont_delete_files, $dont_split_groups, $perc_identity, $output_filename,
$job_runner, $makeblastdb_exec, $mcxdeblast_exec, $mcl_exec, $blastp_exec,
$apply_unknowns_filter, $cpus, $output_multifasta_files, $verbose_stats, $translation_table,
$run_qc, $core_definition, $help
);

GetOptionsFromArray(
$self->args,
Expand All @@ -56,7 +62,7 @@ sub BUILD {
'm|makeblastdb_exec=s' => \$makeblastdb_exec,
'b|blastp_exec=s' => \$blastp_exec,
'd|mcxdeblast_exec=s' => \$mcxdeblast_exec,
'c|mcl_exec=s' => \$mcl_exec,
'c|mcl_exec=s' => \$mcl_exec,
'p|processors=i' => \$cpus,
'apply_unknowns_filter=i' => \$apply_unknowns_filter,
'e|output_multifasta_files' => \$output_multifasta_files,
Expand All @@ -68,17 +74,26 @@ sub BUILD {
't|translation_table=i' => \$translation_table,
'group_limit=i' => \$group_limit,
'qc|run_qc' => \$run_qc,
'dont_run_qc' => \$dont_run_qc,
'dont_run_qc' => \$dont_run_qc,
'cd|core_definition=i' => \$core_definition,
'v|verbose' => \$verbose,
'v|verbose' => \$verbose,
'h|help' => \$help,
);

$self->help($help) if(defined($help));
if ( @{ $self->args } == 0 ) {
$self->_error_message("Error: You need to provide a GFF file");
}

print "\nPlease cite Roary if you use any of the results it produces:
\"Roary: Rapid large-scale prokaryote pan genome analysis\",
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Jacqueline A. Keane, Julian Parkhill,
bioRxiv doi: http://dx.doi.org/10.1101/019315\n\n";

if ( defined($verbose) ) {
$self->verbose($verbose);
$self->logger->level(10000);
}
$self->help($help) if ( defined($help) );
if(@{$self->args} == 0)
{
$self->logger->error("Error: You need to provide a GFF file");
}
$self->output_filename($output_filename) if ( defined($output_filename) );
$self->job_runner($job_runner) if ( defined($job_runner) );
$self->makeblastdb_exec($makeblastdb_exec) if ( defined($makeblastdb_exec) );
Expand All @@ -87,58 +102,50 @@ sub BUILD {
$self->mcl_exec($mcl_exec) if ( defined($mcl_exec) );
$self->cpus($cpus) if ( defined($cpus) );
$self->perc_identity($perc_identity) if ( defined($perc_identity) );
$self->apply_unknowns_filter($apply_unknowns_filter) if ( defined($apply_unknowns_filter) );
if ( defined($output_multifasta_files) )
{
if(which('revtrans.py'))
{
$self->output_multifasta_files($output_multifasta_files) ;
}
else
{
print "WARNING: revtrans.py not found in your PATH so cannot generate multiFASTA alignments, skipping for now.\n";
}
}
$self->dont_delete_files($dont_delete_files) if ( defined($dont_delete_files) );
$self->dont_split_groups($dont_split_groups) if ( defined($dont_split_groups) );
$self->dont_create_rplots(0) if ( defined($create_rplots) );
$self->verbose_stats($verbose_stats) if ( defined $verbose_stats );
$self->translation_table($translation_table) if ( defined($translation_table) );
$self->group_limit($group_limit) if ( defined($group_limit) );
$self->verbose($verbose) if ( defined($verbose) );

if ( defined( $run_qc ) )
{
if(which('kraken') && which('kraken-report'))
{
$self->run_qc($run_qc) ;
}
else
{
print "WARNING: kraken or kraken-report not found in your PATH so cannot run QC, skipping for now.\n";
}
}

if($self->cpus > 1)
{
$self->job_runner('Parallel');
}

$self->core_definition( $core_definition/100 ) if ( defined($core_definition) );
$self->apply_unknowns_filter($apply_unknowns_filter)
if ( defined($apply_unknowns_filter) );

if ( defined($output_multifasta_files) ) {
if ( which('revtrans.py') ) {
$self->output_multifasta_files($output_multifasta_files);
}
else {
$self->logger->warn("revtrans.py not found in your PATH so cannot generate multiFASTA alignments, skipping for now.");
}
}
$self->dont_delete_files($dont_delete_files) if ( defined($dont_delete_files) );
$self->dont_split_groups($dont_split_groups) if ( defined($dont_split_groups) );
$self->dont_create_rplots(0) if ( defined($create_rplots) );
$self->verbose_stats($verbose_stats) if ( defined $verbose_stats );
$self->translation_table($translation_table) if ( defined($translation_table) );
$self->group_limit($group_limit) if ( defined($group_limit) );


if ( defined($run_qc) ) {
if ( which('kraken') && which('kraken-report') ) {
$self->run_qc($run_qc);
}
else {
$self->logger->warn("kraken or kraken-report not found in your PATH so cannot run QC, skipping for now.");
}
}

if ( $self->cpus > 1 ) {
$self->job_runner('Parallel');
}

$self->core_definition( $core_definition / 100 ) if ( defined($core_definition) );

for my $filename ( @{ $self->args } ) {
if ( !-e $filename ) {
$self->_error_message("Error: Cant access file $filename");
$self->logger->error("Error: Cant access file $filename");
last;
}
}
$self->fasta_files( $self->args );

}




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

Expand All @@ -147,24 +154,24 @@ sub run {
print $self->_error_message . "\n";
die $self->usage_text;
}
print "Extracting proteins from GFF files\n" if($self->verbose);

$self->logger->info("Extracting proteins from GFF files");
my $prepare_input_files = Bio::Roary::PrepareInputFiles->new(
input_files => $self->fasta_files,
job_runner => $self->job_runner,
apply_unknowns_filter => $self->apply_unknowns_filter,
cpus => $self->cpus,
translation_table => $self->translation_table,
verbose => $self->verbose
input_files => $self->fasta_files,
job_runner => $self->job_runner,
apply_unknowns_filter => $self->apply_unknowns_filter,
cpus => $self->cpus,
translation_table => $self->translation_table,
verbose => $self->verbose
);

if( $self->run_qc ){
print "Running Kraken on each input assembly\n" if($self->verbose);
if ( $self->run_qc ) {
$self->logger->info("Running Kraken on each input assembly");
my $qc_input_files = Bio::Roary::QC::Report->new(
input_files => $self->fasta_files,
job_runner => $self->job_runner,
cpus => $self->cpus,
verbose => $self->verbose
cpus => $self->cpus,
verbose => $self->verbose
);
$qc_input_files->report;
}
Expand All @@ -186,8 +193,8 @@ sub run {
translation_table => $self->translation_table,
group_limit => $self->group_limit,
core_definition => $self->core_definition,
verbose => $self->verbose
);
verbose => $self->verbose
);
$pan_genome_obj->run();
}

Expand Down
27 changes: 20 additions & 7 deletions lib/Bio/Roary/ExtractProteomeFromGFF.pm
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Expand Up @@ -35,6 +35,7 @@ has '_working_directory' =>
( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
has '_working_directory_name' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__working_directory_name' );
has 'translation_table' => ( is => 'rw', isa => 'Int', default => 11 );
has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' );

sub _build_fasta_file
{
Expand Down Expand Up @@ -90,8 +91,10 @@ sub _create_bed_file_from_gff {
my $cmd =
'sed -n \'/##gff-version 3/,/##FASTA/p\' '
. $self->gff_file
.' | awk \'BEGIN {FS="\t"};{ if ($3 ~/'. $self->_tags_to_filter. '/) print $0;}\' '
. ' | grep -v \'^#\' | awk \'{if ($5 - $4 >= '.$self->min_gene_size_in_nucleotides.') print $1"\t"($4-1)"\t"($5)"\t"$9"\t1\t"$7}\' | sed \'s/ID=//\' | sed \'s/;[^\t]*\t/\t/g\' > '
. $self->_bed_output_filename;
$self->logger->debug($cmd);
system($cmd);
}

Expand All @@ -102,6 +105,7 @@ sub _create_nucleotide_fasta_file_from_gff {
. $self->gff_file
. ' | grep -v \'##FASTA\' > '
. $self->_nucleotide_fasta_file_from_gff_filename;
$self->logger->debug($cmd);
system($cmd);
}

Expand All @@ -119,10 +123,12 @@ sub _extract_nucleotide_regions {
. ' -fo '
. $self->_extracted_nucleotide_fasta_file_from_bed_filename
. ' -name > /dev/null 2>&1';
system($cmd);
unlink($self->_nucleotide_fasta_file_from_gff_filename);
unlink($self->_bed_output_filename);
unlink($self->_nucleotide_fasta_file_from_gff_filename.'.fai');

$self->logger->debug($cmd);
system($cmd);
unlink($self->_nucleotide_fasta_file_from_gff_filename);
unlink($self->_bed_output_filename);
unlink($self->_nucleotide_fasta_file_from_gff_filename.'.fai');
}

sub _cleanup_fasta {
Expand Down Expand Up @@ -170,15 +176,13 @@ sub _convert_nucleotide_to_protein
unlink($self->_extracted_nucleotide_fasta_file_from_bed_filename);
}



sub _does_sequence_contain_too_many_unknowns
{
my ($self, $sequence_obj) = @_;
my $maximum_number_of_Xs = int(($sequence_obj->length()*$self->maximum_percentage_of_unknowns)/100);
my $number_of_Xs_found = () = $sequence_obj->seq() =~ /X/g;
if($number_of_Xs_found > $maximum_number_of_Xs)
{
{
return 1;
}
else
Expand All @@ -194,6 +198,8 @@ sub _filter_fasta_sequences
my $temp_output_file = $filename.'.tmp.filtered.fa';
my $out_fasta_obj = Bio::SeqIO->new( -file => ">".$temp_output_file, -format => 'Fasta');
my $fasta_obj = Bio::SeqIO->new( -file => $filename, -format => 'Fasta');

my $sequence_found = 0;

while(my $seq = $fasta_obj->next_seq())
{
Expand All @@ -203,7 +209,14 @@ sub _filter_fasta_sequences
}
$seq->desc(undef);
$out_fasta_obj->write_seq($seq);
$sequence_found = 1;
}

if($sequence_found == 0)
{
$self->logger->error("Could not extract any protein sequences from ".$self->gff_file.". Does the file contain the assembly as well as the annotation?");
}

# Replace the original file.
move($temp_output_file, $filename);
return 1;
Expand Down
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