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Merge pull request #143 from andrewjpage/blast_errors
Fix input files with duplicate IDs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,162 @@ | ||
| package Bio::Roary::ReformatInputGFFs; | ||
|
|
||
| # ABSTRACT: Take in gff files and add suffix where a gene id is seen twice | ||
|
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| =head1 SYNOPSIS | ||
| Take in gff files and add suffix where a gene id is seen twice | ||
| use Bio::Roary::ReformatInputGFFs; | ||
| my $obj = Bio::Roary::PrepareInputFiles->new( | ||
| gff_files => ['abc.gff','ddd.faa'], | ||
| ); | ||
| $obj->fix_duplicate_gene_ids; | ||
| $obj->fixed_gff_files; | ||
| =cut | ||
|
|
||
| use Moose; | ||
| use Bio::Roary::Exceptions; | ||
| use Cwd; | ||
| use Log::Log4perl qw(:easy); | ||
| use Bio::Tools::GFF; | ||
| use File::Path qw(make_path); | ||
| use File::Basename; | ||
|
|
||
| has 'gff_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); | ||
| has 'logger' => ( is => 'ro', lazy => 1, builder => '_build_logger' ); | ||
| has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' ); | ||
| has 'output_directory' => ( is => 'ro', isa => 'Str', default => 'fixed_input_files' ); | ||
| has 'suffix_counter' => ( is => 'rw', isa => 'Int', default => 1 ); | ||
|
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||
| has 'fixed_gff_files' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] } ); | ||
|
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||
| sub _build_logger { | ||
| my ($self) = @_; | ||
| Log::Log4perl->easy_init( level => $ERROR ); | ||
| my $logger = get_logger(); | ||
| return $logger; | ||
| } | ||
|
|
||
| sub fix_duplicate_gene_ids { | ||
| my ($self) = @_; | ||
|
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||
| my %gene_ids_seen_before; | ||
| for my $file ( @{ $self->gff_files } ) { | ||
|
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| my $ids_seen = 0; | ||
| my $ids_from_file = $self->_get_ids_for_gff_file($file); | ||
|
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| if ( @{$ids_from_file} < 1 ) { | ||
| $self->logger->warn( | ||
| "Input GFF file doesnt contain annotation we can use so excluding it from the analysis: $file" | ||
| ); | ||
| } | ||
| else { | ||
| for my $gene_id ( @{$ids_from_file} ) { | ||
| if ( $gene_ids_seen_before{$gene_id} ) { | ||
| $self->logger->warn( | ||
| "Input file contains duplicate gene IDs, attempting to fix by adding a unique suffix. New GFF in the fixed_input_files directory. $file " | ||
| ); | ||
| my $updated_file = $self->_add_suffix_to_gene_ids_and_return_new_file($file); | ||
| push( @{ $self->fixed_gff_files }, $updated_file ) if ( defined($updated_file) ); | ||
| $ids_seen = 1; | ||
| last; | ||
| } | ||
| $gene_ids_seen_before{$gene_id}++; | ||
| } | ||
| if ( $ids_seen == 0 ) { | ||
| push( @{ $self->fixed_gff_files }, $file ); | ||
| } | ||
| } | ||
| } | ||
| return 1; | ||
| } | ||
|
|
||
| sub _add_suffix_to_gene_ids_and_return_new_file { | ||
| my ( $self, $input_file ) = @_; | ||
| my ( $filename, $directories, $suffix ) = fileparse( $input_file, qr/\.[^.]*/ ); | ||
| make_path( $self->output_directory ) if ( !( -d $self->output_directory ) ); | ||
| my $output_file = $self->output_directory . '/' . $filename . $suffix; | ||
|
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| open( my $input_gff_fh, $input_file ); | ||
| open( my $out_gff_fh, '>', $output_file ); | ||
|
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| my $found_fasta = 0; | ||
| while (<$input_gff_fh>) { | ||
| my $line = $_; | ||
|
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| if ( $line =~ /^\#\#FASTA/ ) { | ||
| $found_fasta = 1; | ||
| } | ||
|
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| if ( $line =~ /\#/ || $found_fasta == 1 ) { | ||
| print {$out_gff_fh} $line; | ||
| next; | ||
| } | ||
|
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| my @cells = split( /\t/, $line ); | ||
| my @tags = split( /;/, $cells[8] ); | ||
| my $found_id = 0; | ||
| for ( my $i = 0 ; $i < @tags ; $i++ ) { | ||
| if ( $tags[$i] =~ /^(ID=["']?)([^;"']+)(["']?)/ ) { | ||
| my $current_id = $2; | ||
| $current_id .= '___' . $self->suffix_counter; | ||
| $tags[$i] = $1 . $current_id . $3; | ||
| $self->suffix_counter( $self->suffix_counter + 1 ); | ||
| $found_id++; | ||
| last; | ||
| } | ||
| } | ||
| if ( $found_id == 0 ) { | ||
| unshift( @tags, 'ID=id___' . $self->suffix_counter ); | ||
| $self->suffix_counter( $self->suffix_counter + 1 ); | ||
| } | ||
| $cells[8] = join( ';', @tags ); | ||
| print {$out_gff_fh} join( "\t", @cells ); | ||
| } | ||
|
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||
| if ( $found_fasta == 0 ) { | ||
| $self->logger->warn( | ||
| "Input GFF file doesnt appear to have the FASTA sequence at the end of the file so is being excluded from the analysis: $input_file" ); | ||
| return undef; | ||
| } | ||
| close($out_gff_fh); | ||
| close($input_gff_fh); | ||
| return $output_file; | ||
| } | ||
|
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||
| sub _get_ids_for_gff_file { | ||
| my ( $self, $file ) = @_; | ||
| my @gene_ids; | ||
| my $tags_regex = $self->_tags_to_filter; | ||
| my $gffio = Bio::Tools::GFF->new( -file => $file, -gff_version => 3 ); | ||
| while ( my $feature = $gffio->next_feature() ) { | ||
| next if !( $feature->primary_tag =~ /$tags_regex/ ); | ||
| my $gene_id = $self->_get_feature_id($feature); | ||
| push( @gene_ids, $gene_id ) if ( defined($gene_id) ); | ||
| } | ||
| return \@gene_ids; | ||
| } | ||
|
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||
| sub _get_feature_id { | ||
| my ( $self, $feature ) = @_; | ||
| my ( $gene_id, @junk ); | ||
| if ( $feature->has_tag('ID') ) { | ||
| ( $gene_id, @junk ) = $feature->get_tag_values('ID'); | ||
| } | ||
| elsif ( $feature->has_tag('locus_tag') ) { | ||
| ( $gene_id, @junk ) = $feature->get_tag_values('locus_tag'); | ||
| } | ||
| else { | ||
| return undef; | ||
| } | ||
| $gene_id =~ s!["']!!g; | ||
| return undef if ( $gene_id eq "" ); | ||
| return $gene_id; | ||
| } | ||
|
|
||
| no Moose; | ||
| __PACKAGE__->meta->make_immutable; | ||
|
|
||
| 1; |
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