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@@ -43,5 +43,5 @@ | |
| } | ||
| }, | ||
| "release_status" : "stable", | ||
| "version" : "v2.2.0" | ||
| "version" : "v3.0.0" | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -25,4 +25,4 @@ requires: | |
| Pod::Coverage: '0.23' | ||
| Template: '2.26' | ||
| Test::Fatal: '0.013' | ||
| version: v2.2.0 | ||
| version: v3.0.0 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,210 @@ | ||
| #!/usr/bin/perl | ||
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||
| use strict; | ||
| use warnings FATAL => 'all'; | ||
| use autodie; | ||
| use Const::Fast qw(const); | ||
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||
| const my @NEW_BEDPE_HEADER => ('# chr1','start1','end1','chr2','start2','end2','id/name','brass_score','assembly_score','strand1','strand2','sample','readpair names','readpair count','bal_trans','inv','occL','occH','copynumber_flag','range_blat','Brass Notation','non-template','micro-homology','assembled readnames','assembled read count','gene','gene_id','transcript_id','strand','end_phase','region','region_number','total_region_count','first/last','gene','gene_id','transcript_id','strand','phase','region','region_number','total_region_count','first/last','fusion_flag'); | ||
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| if(scalar @ARGV != 3) { | ||
| warn "USAGE: combineResults.pl X_ann.groups X_ann.assembled X.final\n"; | ||
| warn "\tX.final is a prefix, relevant suffixes will be added for VCF and BEDPE outputs\n"; | ||
| exit 1; | ||
| } | ||
| my ($groups_prefix, $assembled_prefix, $final_prefix) = @ARGV; | ||
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| mergeVcf($groups_prefix, $assembled_prefix, $final_prefix); | ||
| mergeBedpe($groups_prefix, $assembled_prefix, $final_prefix); | ||
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| sub mergeVcf { | ||
| my ($groups_prefix, $assembled_prefix, $final_prefix) = @_; | ||
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| my $assembled_vcf = "$assembled_prefix.vcf"; | ||
| my $phaseI_vcf = "$groups_prefix.vcf"; | ||
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| my $final_vcf = "$final_prefix.vcf"; | ||
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| my %orig_data; | ||
| open my $ORIG, '<', $assembled_vcf; | ||
| while(my $line = <$ORIG>) { | ||
| next if($line =~ m/^#/); | ||
| chomp $line; | ||
| my @bits = split /\t/, $line; | ||
| my $id = $bits[2]; | ||
| $orig_data{$id} = \@bits; | ||
| } | ||
| close $ORIG; | ||
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| my $new_info = q{##INFO=<ID=BAS,Number=.,Type=Integer,Description="Brass Assembly Score:A maximum score of 100 indicates a perfect pattern of 5 vertices in Velvet's de Bruijn graph">} | ||
| .qq{\n} | ||
| .q{##INFO=<ID=SVCLASS,Number=.,Type=String,Description="basic SV class, deletion, inversion, tandem-duplication">}; | ||
| my $new_format = q{##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Count of pairs that span this breakpoint">}; | ||
|
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| my $info_found = 0; | ||
| my $format_found = 0; | ||
|
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| open my $FINAL, '>', $final_vcf; | ||
| open my $FIXED, '<', $phaseI_vcf; | ||
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| my @ends; | ||
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| while(my $line = <$FIXED>) { | ||
| if(@ends == 2) { | ||
| svclass(\@ends); | ||
| print $FINAL join("\t",@{$ends[0]}), "\n"; | ||
| print $FINAL join("\t",@{$ends[1]}), "\n"; | ||
| @ends = (); | ||
| } | ||
| if($line =~ m/^#/) { | ||
| if($info_found == 0 && $line =~ m/^##INFO/) { | ||
| print $FINAL $new_info,"\n"; | ||
| $info_found = 1; | ||
| } | ||
| if($format_found == 0 && $line =~ m/^##FORMAT/) { | ||
| print $FINAL $new_format,"\n"; | ||
| $format_found = 1; | ||
| } | ||
| print $FINAL $line; | ||
| next; | ||
| } | ||
| chomp $line; | ||
| my @bits = split /\t/, $line; | ||
| my $id = $bits[2]; | ||
| if(!exists $orig_data{$id}) { | ||
| $bits[-3] .= ':PS'; | ||
| $bits[-2] = '0:'.$bits[-2]; # normal is always 0:0 | ||
| $bits[-1] = '0:'.$bits[-1]; | ||
|
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| push @ends, \@bits; | ||
| next; | ||
| } | ||
| else { | ||
| my $old_info = $orig_data{$id}->[7]; | ||
| my ($tsrds) = $bits[7] =~ m/(TSRDS=[^;]+)/; | ||
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| $bits[7] = $old_info.';'.$tsrds; | ||
| $bits[7] .= ';BAS='.$orig_data{$id}->[5]; | ||
| $bits[5] = q{.}; | ||
| $bits[-3] .= ':PS'; | ||
| $bits[-2] = '0:'.$bits[-2]; # normal is always 0:0 | ||
| $bits[-1] = $orig_data{$id}->[-1].':'.$bits[-1]; | ||
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| $bits[7] =~ s/;;/;/g; | ||
|
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| push @ends, \@bits; | ||
| next; | ||
| } | ||
| } | ||
| if(@ends == 2) { | ||
| svclass(\@ends); | ||
| print $FINAL join("\t",@{$ends[0]}), "\n"; | ||
| print $FINAL join("\t",@{$ends[1]}), "\n"; | ||
| } | ||
|
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||
| close $FIXED; | ||
| close $FINAL; | ||
| } | ||
|
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| sub mergeBedpe { | ||
| my ($groups_prefix, $assembled_prefix, $final_prefix) = @_; | ||
| my $assembled_bedpe = "$assembled_prefix.bedpe"; | ||
| my $phaseI_bedpe= "$groups_prefix.bedpe"; | ||
| my $final_bedpe = "$final_prefix.bedpe"; | ||
|
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| my %orig_data; | ||
| open my $ORIG, '<', $assembled_bedpe; | ||
| while(my $line = <$ORIG>) { | ||
| next if($line =~ m/^#/); | ||
| chomp $line; | ||
| my @bits = split /\t/, $line; | ||
| my $id = $bits[6]; | ||
| $orig_data{$id} = \@bits; | ||
| } | ||
| close $ORIG; | ||
|
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| open my $FINAL, '>', $final_bedpe; | ||
| open my $FIXED, '<', $phaseI_bedpe; | ||
|
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| print $FINAL join("\t", @NEW_BEDPE_HEADER),"\n"; | ||
|
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| while(my $line = <$FIXED>) { | ||
| next if($line =~ m/^#/); | ||
| chomp $line; | ||
| my @bits = split /\t/, $line; | ||
| my $id = $bits[6]; | ||
| if(index($id, ',') != -1) { | ||
| my @ids = split /,/, $id; | ||
| my @multi_record; | ||
| for(@ids) { | ||
| push @multi_record, $orig_data{$id} if(exists $orig_data{$id}); | ||
| } | ||
| if(scalar @multi_record) { | ||
| warn "MULTI\n"; | ||
| warn "$line\n"; | ||
| warn Dumper(\@multi_record); | ||
| } | ||
| die "merged events correlate with assembled results, don't know what to do"; | ||
| } | ||
| elsif(!exists $orig_data{$id}) { | ||
| my @new; | ||
| push @new, @bits[0..7]; # 1-8 | ||
| push @new, q{_}; # 9 | ||
| push @new, @bits[8..9]; # 10-11 | ||
| push @new, $bits[16]; # 12 | ||
| push @new, @bits[18..25]; # 13-20 | ||
| push @new, q{_},q{_},q{_},q{_},q{_}; # 21-25 | ||
| push @new, @bits[26..44]; # 26-44 | ||
|
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| print $FINAL join("\t", @new),"\n"; | ||
| next; | ||
| } | ||
| else { | ||
| my @old_brass_II = @{$orig_data{$id}}; | ||
| my @new; | ||
| push @new, @old_brass_II[0..6]; # 1-7 | ||
| push @new, q{_}; # 8 | ||
| push @new, @old_brass_II[7..10]; # 9-12 | ||
| push @new, @bits[18..25]; # 13-20 | ||
| push @new, @old_brass_II[11..14]; # 21-24 | ||
| push @new, scalar (split /,/, $new[-1]); # 25 # assembled read count | ||
| push @new, @bits[26..44]; # 26-44 | ||
|
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| print $FINAL join("\t", @new),"\n"; | ||
| next; | ||
| } | ||
| } | ||
|
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||
|
|
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| close $FIXED; | ||
| close $FINAL; | ||
|
|
||
| return; | ||
| } | ||
|
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||
|
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||
| sub svclass { | ||
| my ($end_a, $end_b) = @{$_[0]}; | ||
| die "Record IDs out of sync at:\n",join("\t",@{$end_a}),"\n",join("\t",@{$end_b}),"\n" if($end_a->[2] !~ m/_[12]$/ || $end_b->[2] !~ m/_[12]$/); | ||
| my $class; | ||
| if($end_a->[4] =~ m/^[[:upper:]]\[/) { | ||
| # ++ | ||
| $class = 'deletion'; | ||
| } | ||
| elsif($end_a->[4] =~ m/^[[:upper:]]\]/ || $end_a->[4] =~ m/\[[[:upper:]]$/) { | ||
| # +- / -+ | ||
| $class = 'inversion'; | ||
| } | ||
| elsif($end_a->[4] =~ m/\][[:upper:]]$/) { | ||
| # -- | ||
| $class = 'tandem-duplication'; | ||
| } | ||
| else { | ||
| die "Unknown rearrangement syntax: $end_a->[4]\n"; | ||
| } | ||
| $end_a->[7] .= ';SVCLASS='.$class; | ||
| $end_b->[7] .= ';SVCLASS='.$class; | ||
| return; | ||
| } | ||
|
|
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