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更新 targettherpy 添加最后一列

master
chaopower 2024-02-19 16:13:10 +08:00
parent eea6ceb162
commit 39f51ccf2e
5 changed files with 59 additions and 33 deletions
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16
codes/target_therapy_cnv.pl
View File

@ -108,6 +108,10 @@ while (<IN>) {
if ($cn >= 4 and exists $therapy{lc $cnv_detected}{lc 'Amplification'}) {
foreach my $entry (@{$therapy{lc $cnv_detected}{lc 'Amplification'}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
my $dises;
if (!(exists $dis{lc $line[2]})) {
$dises = 'unknow';
@ -116,16 +120,16 @@ while (<IN>) {
$dises = $dis{lc $line[2]};
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症\t" . &drug($line[3]) . "\t" . $dises;
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症\t" . &drug($line[3]) . "\t" . $dises . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症\t" . &drug($line[3]) . "\t" . $dises;
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症\t" . &drug($line[3]) . "\t" . $dises . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dises;
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dises . "\t" . $line[16];
$bool = 1;
}
}
@ -141,15 +145,15 @@ while (<IN>) {
$dises = $dis{lc $line[2]};
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症\t" . &drug($line[3]) . "\t" . $dises;
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症\t" . &drug($line[3]) . "\t" . $dises . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症\t" . &drug($line[3]) . "\t" . $dises;
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症\t" . &drug($line[3]) . "\t" . $dises . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dises;
push @pos, "$_\t$cn\tOncogenic\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dises . "\t" . $line[16];
$bool = 1;
}
}

15
codes/target_therapy_fusion.pl
View File

@ -128,16 +128,19 @@ while (<IN>) {
if (exists $therapy{lc $gene}{lc "$record{'FUSION'} Fusion"}) {
foreach my $entry (@{$therapy{lc $gene}{lc "$record{'FUSION'}Fusion"}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
}
@ -147,15 +150,15 @@ while (<IN>) {
foreach my $entry (@{$therapy{lc $gene}{lc "Fusion"}}) {
my @line = split("\t", $entry);
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
}

10
codes/target_therapy_longindel.pl
View File

@ -106,14 +106,18 @@ while (<IN>) {
if (exists $therapy{lc 'BCL2L11'}{lc 'DELETION POLYMORPHISM'}) {
foreach my $entry (@{$therapy{lc 'BCL2L11'}{lc 'DELETION POLYMORPHISM'}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
}
}

49
codes/target_therapy_snpindel.pl
View File

@ -81,7 +81,7 @@ open VUS, ">$output.vus.txt";
my $h2 = <IN>;
chomp $h2;
my $h = $h2 . "\tfun_change\t" . join("\t", (split("\t", $h1))[0 .. 9, 14]) . "\tLabel\tDrugCn\tIndication";
my $h = $h2 . "\tfun_change\t" . join("\t", (split("\t", $h1))[0 .. 9, 14]) . "\tLabel\tDrugCn\tIndication\treport_need_note";
print POS "$h\n";
print NEG $h2 . "\tfun_change\n";
print VUS $h2 . "\tfun_change\n";
@ -116,7 +116,6 @@ while (<IN>) {
}
elsif ($record{'ExonicFunc_refGene'} =~ /skipping/) {
$protein = 'Exon 14 Skipping Mutation';
print "$protein\n";
$mut_type = '';
}
elsif ($record{'Func_refGene'} =~ /splicing/) {
@ -158,16 +157,20 @@ while (<IN>) {
if (exists $therapy{lc $gene}{lc $protein}) {
foreach my $entry (@{$therapy{lc $gene}{lc $protein}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
}
@ -176,16 +179,19 @@ while (<IN>) {
if (exists $therapy{lc $gene}{'mutation'}) {
foreach my $entry (@{$therapy{lc $gene}{'mutation'}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
}
@ -194,16 +200,19 @@ while (<IN>) {
if ($protein =~ /^(\w\d+)\w$/ and exists $therapy{lc $gene}{lc $1}) {
foreach my $entry (@{$therapy{lc $gene}{lc $1}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
}
@ -212,16 +221,19 @@ while (<IN>) {
if ($protein =~ /^(\w\d+)\w$/ and exists $therapy{lc $gene}{lc $1 . "X"}) {
foreach my $entry (@{$therapy{lc $gene}{lc $1 . "X"}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
}
@ -230,16 +242,19 @@ while (<IN>) {
if (exists $therapy{lc $gene}{lc $mut_type}) {
foreach my $entry (@{$therapy{lc $gene}{lc $mut_type}}) {
my @line = split("\t", $entry);
if (!defined($line[16])) {
$line[16] = '';
}
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
$bool = 1;
}
}

2
wdl/msi.wdl
View File

@ -27,7 +27,7 @@ task run_msi {
echo "msi 624 探针 "
msisensor2 msi \
-M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
-t ${tumor_rmdup_bam} -e $PUBLIC/msi//624_650_intersect_depth50_177.bed -b 10 \
-t ${tumor_rmdup_bam} -e $PUBLIC/msi/624_650_intersect_depth50_177.bed -b 10 \
-o ${output_dir}/msi/${name}.msi.txt
elif [ "${probe}" == "160" ]; then