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[issue/273] dbSNP 2 VCF reformat util (#300)
* Takes N DbSNP 2 VCF files (https://www.ncbi.nlm.nih.gov/snp/docs/products/vcf/redesign/), extracts every population from the Freq=(.*) field in a separate INFO field, drops the Freq field, drops the first allele for each population (which is reference). Then it writes the population-specific fields to the info header, and updates the yml config file to point to the newly formatted vcf (the original vcf will not be overwritten). This is necessary because the dbSNP 2 vcf does not make good use of the VCF spec; the Freq field is the combination of multiple fields, each of which is an Allelic type, but where the first allele is the reference, which is not the standard use. This will enable us to reproducibly fetch, transform, build dbSNP files, from 1 yaml config, once we add 1 more utility, which translates the RefSeq NC_* chromosome identifiers to chr1-22,X,Y,M. Will remove [wip] once test added --------- Co-authored-by: wingolab <thomas.wingo@emory.edu>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,211 @@ | ||
| #!/usr/bin/perl | ||
| use 5.10.0; | ||
| use strict; | ||
| use warnings; | ||
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| # Take a DbSNP 2 VCF file, and for each row, split the INFO field's FREQ data into separate INFO fields for each population | ||
| # NOTE: dbSNP VCF spec: https://www.ncbi.nlm.nih.gov/snp/docs/products/vcf/redesign/ | ||
| # NOTE: that dbSNP uses a '.' to represent a missing value and first allele is the reference, which is not the standard use. | ||
|
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| package Utils::DbSnp2FormatInfo; | ||
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| our $VERSION = '0.001'; | ||
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| use File::Basename qw/basename/; | ||
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| use Mouse 2; | ||
| use namespace::autoclean; | ||
| use Path::Tiny qw/path/; | ||
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| use Seq::Tracks::Build::LocalFilesPaths; | ||
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| # Exports: _localFilesDir, _decodedConfig, compress, _wantedTrack, _setConfig, logPath, use_absolute_path | ||
| extends 'Utils::Base'; | ||
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| my $INFO_INDEX = 7; | ||
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| sub BUILD { | ||
| my $self = shift; | ||
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| my $localFilesHandler = Seq::Tracks::Build::LocalFilesPaths->new(); | ||
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| my $localFilesAref = $localFilesHandler->makeAbsolutePaths( | ||
| $self->_decodedConfig->{files_dir}, | ||
| $self->_wantedTrack->{name}, | ||
| $self->_wantedTrack->{local_files} | ||
| ); | ||
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| $self->{_localFiles} = $localFilesAref; | ||
| } | ||
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| sub _get_fh_paths { | ||
| my ( $self, $input_vcf ) = @_; | ||
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| if ( !-e $input_vcf ) { | ||
| $self->log( 'fatal', "input file path $input_vcf doesn't exist" ); | ||
| return; | ||
| } | ||
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| my ( $err, $isCompressed, $in_fh ) = $self->getReadFh($input_vcf); | ||
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| $isCompressed ||= $self->compress; | ||
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| if ($err) { | ||
| $self->log( 'fatal', $err ); | ||
| return; | ||
| } | ||
|
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| my $base_name = basename($input_vcf); | ||
| $base_name =~ s/\.[^.]+$//; # Remove last file extension (if present) | ||
| $base_name | ||
| =~ s/\.[^.]+$//; # Remove another file extension if it's something like .vcf.gz | ||
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| my $output_vcf_data = $base_name . "_vcf_data.vcf" . ( $isCompressed ? ".gz" : "" ); | ||
| my $output_vcf_header = | ||
| $base_name . "_vcf_header.vcf" . ( $isCompressed ? ".gz" : "" ); | ||
| my $output_vcf = $base_name . "_processed.vcf" . ( $isCompressed ? ".gz" : "" ); | ||
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| $self->log( 'info', "Reading $input_vcf" ); | ||
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| my $output_header_path = | ||
| path( $self->_localFilesDir )->child($output_vcf_header)->stringify(); | ||
| my $output_data_path = | ||
| path( $self->_localFilesDir )->child($output_vcf_data)->stringify(); | ||
| my $output_path = path( $self->_localFilesDir )->child($output_vcf)->stringify(); | ||
|
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| if ( ( -e $output_data_path || -e $output_header_path || -e $output_path ) | ||
| && !$self->overwrite ) | ||
| { | ||
| $self->log( 'fatal', | ||
| "Temp files $output_data_path, $output_header_path, or final output path $output_path exist, and overwrite is not set" | ||
| ); | ||
| return; | ||
| } | ||
|
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| return ( $in_fh, $output_data_path, $output_header_path, $output_path ); | ||
| } | ||
|
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| sub go { | ||
| my $self = shift; | ||
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| my @output_paths; | ||
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| for my $input_vcf ( @{ $self->{_localFiles} } ) { | ||
| my ( $in_fh, $output_data_path, $output_header_path, $output_path ) = | ||
| $self->_get_fh_paths($input_vcf); | ||
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| my $output_data_fh = $self->getWriteFh($output_data_path); | ||
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| $self->log( 'info', "Writing to $output_data_path" ); | ||
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| my %populations; | ||
| my @ordered_populations; | ||
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| my @header_lines; | ||
| while (<$in_fh>) { | ||
| chomp; | ||
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| # If it's a header line | ||
| if (/^#/) { | ||
| push @header_lines, $_; | ||
| next; | ||
| } | ||
|
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| my @fields = split( "\t", $_ ); | ||
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| if ( !@fields ) { | ||
| $self->log( "fatal", "No fields found in row: $_" ); | ||
| return; | ||
| } | ||
|
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| my @info_fields = split( ";", $fields[$INFO_INDEX] ); | ||
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| my @ordered_info_freqs; | ||
| my %seen_info_pops; | ||
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| my $seen_freq = 0; | ||
| foreach my $info (@info_fields) { | ||
| if ( $info =~ /FREQ=(.+)/ ) { | ||
| if ( $seen_freq == 1 ) { | ||
| $self->log( "fatal", "FREQ seen twice in INFO field. Row: $_" ); | ||
| return; | ||
| } | ||
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| $seen_freq = 1; | ||
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| my $freq_data = $1; | ||
| my @pops = split( /\|/, $freq_data ); | ||
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| foreach my $pop (@pops) { | ||
| if ( $pop =~ /([^:]+):(.+)/ ) { | ||
| my $pop_name = $1; | ||
|
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| if ( exists $seen_info_pops{$pop_name} ) { | ||
| self->log( "fatal", "Population $pop_name seen twice in INFO field. Row: $_" ); | ||
| return; | ||
| } | ||
|
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| my @freq_vals = split( /,/, $2 ); | ||
| shift @freq_vals; # Remove the reference allele freq | ||
|
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| push @ordered_info_freqs, [ $pop_name, join( ",", @freq_vals ) ]; | ||
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| if ( !exists $populations{$pop_name} ) { | ||
| push @ordered_populations, $pop_name; | ||
| $populations{$pop_name} = 1; | ||
| } | ||
| } | ||
| } | ||
|
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| # Append the new frequency data to the INFO field | ||
| my @new_info_fields; | ||
| for my $res (@ordered_info_freqs) { | ||
| my $name = $res->[0]; | ||
| my $freq = $res->[1]; | ||
| push @new_info_fields, "$name=$freq"; | ||
| } | ||
|
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| $info = join( ";", @new_info_fields ); | ||
| } | ||
| } | ||
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| $fields[$INFO_INDEX] = join( ";", @info_fields ); | ||
|
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| say $output_data_fh join( "\t", @fields ); | ||
| } | ||
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| close($in_fh); | ||
| close($output_data_fh); | ||
|
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| # Update the VCF header with new populations | ||
| my @pop_lines; | ||
| foreach my $pop (@ordered_populations) { | ||
| push @pop_lines, | ||
| "##INFO=<ID=$pop,Number=A,Type=Float,Description=\"Frequency for $pop\">"; | ||
| } | ||
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| splice( @header_lines, -1, 0, @pop_lines ); | ||
|
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| my $header_fh = $self->getWriteFh($output_header_path); | ||
|
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| # Write the updated header and VCF to output | ||
| say $header_fh join( "\n", @header_lines ); | ||
| close($header_fh); | ||
|
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| system("cat $output_header_path $output_data_path > $output_path") == 0 | ||
| or die "Failed to concatenate files: $?"; | ||
| system("rm $output_header_path $output_data_path") == 0 | ||
| or die "Failed to remove temporary files: $?"; | ||
|
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| $self->log( 'info', "$input_vcf processing complete" ); | ||
|
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| push @output_paths, $output_path; | ||
| } | ||
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| $self->_wantedTrack->{local_files} = \@output_paths; | ||
|
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| $self->_backupAndWriteConfig(); | ||
| } | ||
|
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| __PACKAGE__->meta->make_immutable; | ||
| 1; |
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