添加pollution
parent
2a9eff2226
commit
b9685fd29e
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21
pipeline.wdl
21
pipeline.wdl
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@ -1,5 +1,4 @@
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import "./wdl/catecode.wdl"
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import "./wdl/qc.wdl"
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import "./wdl/alignment.wdl"
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import "./wdl/call_mutation.wdl"
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@ -12,6 +11,7 @@ import "./wdl/hereditary.wdl"
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import "./wdl/tmb.wdl"
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import "./wdl/postprocess.wdl"
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workflow pipeline {
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String tumor
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@ -33,10 +33,10 @@ workflow pipeline {
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Map[String, Boolean] catecode
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# call mytask.create_dir as create_dir {
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# input:
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# workdir=workdir
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# }
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# call mytask.create_dir as create_dir {
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# input:
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# workdir=workdir
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# }
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call qc.qc as qc {
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input:
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@ -168,6 +168,17 @@ workflow pipeline {
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project=project
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}
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call pollution.call_pollution as call_pollution {
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input:
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name=tumor,
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normal=normal,
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output_dir=workdir,
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probe=probe,
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raw_vcf=call_mutation.raw_vcf,
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somatic_vcf=call_mutation.somatic_vcf,
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germline_vcf=call_mutation.germline_vcf
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}
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call postprocess.call_postprocess as call_postprocess {
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input:
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run=catecode['addAutoReport'],
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@ -225,8 +225,7 @@ class ChemoRun:
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if __name__ == "__main__":
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parser = argparse.ArgumentParser(description="Chemotherapy Process Script")
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parser.add_argument('-d', '--database', help="Path to chemo_drug's database",
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default='/home/zhangchao/project/pipeline/workflow/script/public/chemo_database.xlsx')
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parser.add_argument('-d', '--database', help="Path to chemo_drug's database", required=True)
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parser.add_argument('-probe', '--probe', help="Probe name", required=True)
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parser.add_argument('-n', '--name', help="Name for sample", required=True)
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parser.add_argument('-v', '--vcf', help="germline vcf", required=True)
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@ -7,9 +7,10 @@ open IN, "$ARGV[0]";
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open OUT, ">$ARGV[1]";
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my $project = $ARGV[2];
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my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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# my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "Cnv过滤使用public路径：$public_path\n";
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print "Cnv过滤使用database路径：$database_path\n";
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my $cnv = info();
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my @cnv_list = @$cnv;
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@ -22,7 +23,7 @@ print OUT join("\t", (@head[0 .. 4], "ref_gene", "copy", @head[5 .. 9])), "\n";
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while (<IN>) {
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chomp;
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my @line = split(/\t/, $_);
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my $cn = sprintf("%.2f", 2 ** (1 + $line[4]));
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my $cn = sprintf("%.1f", 2 ** (1 + $line[4]));
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my @gene_list = split(/,/, $line[3]);
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my %uniq;
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foreach my $element (@gene_list) {
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@ -38,7 +39,7 @@ while (<IN>) {
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}
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sub info {
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open INFO, "$public_path/info.csv";
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open INFO, "$database_path/info.csv";
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# 读取并解析表头
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my $header = <INFO>;
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chomp($header);
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@ -6,8 +6,10 @@ die "usage:perl $0 depth_file input out project" unless @ARGV == 4;
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my ($depth_file, $input, $out, $project) = @ARGV;
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my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "Fusion过滤使用public路径：$public_path\n";
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print "Fusion过滤使用database路径：$database_path\n";
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open IN, "$input";
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open OUT1, "> $out";
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@ -189,7 +191,7 @@ sub gene2strand {
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}
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sub info {
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open INFO, "$public_path/info.csv";
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open INFO, "$database_path/info.csv";
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# 读取并解析表头
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my $header = <INFO>;
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chomp($header);
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@ -4,9 +4,12 @@ use warnings;
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die "usage:perl $0 input out project" unless @ARGV == 3;
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my ($input, $out, $project) = @ARGV;
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my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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# my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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#
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# print "LongIndel过滤使用public路径：$public_path\n";
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "LongIndel过滤使用public路径：$public_path\n";
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print "longindel过滤使用database路径：$database_path\n";
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open IN, "$input";
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open LONGINDEL, "> $out";
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@ -40,7 +43,7 @@ while (<IN>) {
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}
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sub info {
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open INFO, "$public_path/info.csv";
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open INFO, "$database_path/info.csv";
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# 读取并解析表头
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my $header = <INFO>;
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chomp($header);
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@ -0,0 +1,52 @@
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#!/usr/bin/env perl
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use strict;
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my ($name, $output_dir, $project) = @ARGV;
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die "useage:perl $0 codes_dir name output_dir project" unless @ARGV == 4;
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my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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open INFO, "$public_path/info.csv";
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<INFO>;
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my @promoter;
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while (<INFO>) {
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chomp;
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my @line = split(/\t/, $_);
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if ($line[0] eq $project) {
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if ($line[4] ne "NA") {
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@promoter = split(/\//, $line[4]);
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open PRMT, ">$output_dir/mutation/${name}.target.promoter.txt";
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}
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}
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}
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my @prmt;
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open IN2, "$output_dir/mutation/${name}.snp.indel.Somatic.annoall.hg19_multianno.txt";
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<IN2>;
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while (<IN2>) {
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chomp;
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my @line = split(/\t/, $_);
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if (@promoter and grep {$line[6] eq $_} @promoter) {
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if ($line[5] =~ /UTR3|upstream/ and $line[17] < 0.01
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and $line[18] < 0.01 and $line[19] < 0.01 and $line[20] < 0.01 and $line[23] < 0.01 and $line[28] < 0.01 and $line[32] < 0.01) {
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my @var = split(/;/, $line[9]);
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my $freq = (split(/:/, $line[-2]))[5];
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my $dp4 = join(",", (split(/:/, $line[-2]))[2, 4, -1]);
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my $predict_benign = 0;
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$predict_benign++ if ($line[50] eq "N" or $line[50] eq "P");
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$predict_benign++ if $line[56] eq "T";
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$predict_benign++ if $line[64] eq "T";
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if ($line[6] eq 'TERT') {
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push @prmt, join("\t", @line[0 .. 9], $freq, $dp4, $predict_benign, @line[10, 11, 16, 18, $#line])
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if (($line[1] eq '1295228' and $line[4] eq 'A') or ($line[1] eq '1295250' and $line[4] eq 'A'));
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}
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}
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}
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}
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if (@prmt) {
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print PRMT join("\t", @head[0 .. 9]), "\tFreq", "\tDP-AD-DP4", "\tpredict_benign(MutationTaster/FATHMM/MetaSVM)\t", join("\t", @head[10, 11, 16, 18]), "\tSTR", "\n";
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print PRMT join("\n", @prmt) . "\n";
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}
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@ -243,7 +243,7 @@ sub blacklist {
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sub info {
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open INFO, "$public_path/info.csv";
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open INFO, "$database_path/info.csv";
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# 读取并解析表头
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my $header = <INFO>;
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chomp($header);
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@ -65,8 +65,7 @@ class HereditaryRun:
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if __name__ == "__main__":
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parser = argparse.ArgumentParser(description="hereditary Process Script")
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parser.add_argument('-d', '--database', help="Path to hereditary_mut's database",
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default='/home/zhangchao/project/pipeline/workflow/script/public/hereditary_database.xlsx')
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parser.add_argument('-d', '--database', help="Path to hereditary_mut's database", required=True)
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parser.add_argument('-p', '--project', help="Project name", required=True)
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parser.add_argument('-n', '--name', help="Name for sample", required=True)
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parser.add_argument('-f', '--file', help="germline filter file", required=True)
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@ -2,14 +2,14 @@
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use strict;
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use warnings;
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my ($output_dir,$cancer_type)=@ARGV;
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die "useage:perl $0 output_dir cancer_type" unless @ARGV==2;
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my ($output_dir, $cancer_type) = @ARGV;
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die "useage:perl $0 output_dir cancer_type" unless @ARGV == 2;
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "Indication药物注释使用路径：$database_path\n";
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open OUT,">$output_dir/mutation/indication.txt";
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open OUT, ">$output_dir/mutation/indication.txt";
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print OUT "基因\t检测内容\t检测情况\t肿瘤类型\n";
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##本癌种FDA/NMPA/NCCN批准基因检测
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=pod
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@ -26,56 +26,58 @@ while(<DIS>){
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}
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=cut
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open DIS,"/dataseq/jmdna/codes/reportbase/oncotree.cancertype.20230801.txt";
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open DIS, "$database_path/oncotree.cancertype.20230801.txt";
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<DIS>;
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my (%dis,@id,%dis2);
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while(<DIS>){
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my (%dis, @id, %dis2);
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while (<DIS>) {
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chomp;
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my @line=split(/\t/);
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$dis{lc$line[2]}=$line[3];
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$dis{lc$line[4]}=$line[5];
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push @{$dis2{$line[0]}},lc$line[2];
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push @{$dis2{$line[0]}},lc$line[4];
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push @id,$line[0];
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my @line = split(/\t/);
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$dis{lc $line[2]} = $line[3];
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# $dis{lc $line[4]} = $line[5];
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push @{$dis2{$line[0]}}, lc $line[2];
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# push @{$dis2{$line[0]}}, lc $line[4];
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push @id, $line[0];
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}
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foreach my $ID($cancer_type){
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foreach my $ID ($cancer_type) {
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my @family;
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my @ids=split("",$ID);
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for (my $i=1;$i<@ids;$i=$i+2){
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push @family,join("",@ids[0..$i]);
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my @ids = split("", $ID);
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for (my $i = 1; $i < @ids; $i = $i + 2) {
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push @family, join("", @ids[0 .. $i]);
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}
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push @family,(grep{/^$ID/}@id);
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foreach my $t(@family){
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push @{$dis2{$ID}},@{$dis2{$t}};
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push @family, (grep {/^$ID/} @id);
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foreach my $t (@family) {
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push @{$dis2{$ID}}, @{$dis2{$t}};
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}
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}
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foreach my $key(keys(%dis2)){
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foreach my $key (keys(%dis2)) {
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my %uniq;
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@{$dis2{$key}}=grep{++$uniq{$_}<2}@{$dis2{$key}};
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@{$dis2{$key}} = grep {++$uniq{$_} < 2} @{$dis2{$key}};
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}
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##靶向用药信息
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open THERAPY,"$database_path/targetTherapy.txt";
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<THERAPY>;
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open THERAPY, "$database_path/targetTherapy.txt";
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<THERAPY>;
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my %therapy;
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my %cancer;
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while(<THERAPY>){
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while (<THERAPY>) {
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chomp;
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my @line=split("\t");
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if($line[9] eq 'V' and $line[14] eq 'A' and (grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}) and $line[0]!~/,/){
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push @{$cancer{$line[0]}},$dis{lc$line[2]} if !(grep{$_ eq $dis{lc$line[2]}}@{$cancer{$line[0]}});
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if($line[1]=~/fusion/i){
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push @{$therapy{$line[0]}},'融合' if !(grep{$_ eq '融合'}@{$therapy{$line[0]}});
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}elsif($line[1] eq "Deletion" or $line[1]=~ /Amplification/){
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push @{$therapy{$line[0]}},'扩增' if !(grep{$_ eq '扩增'}@{$therapy{$line[0]}});
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}else{
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push @{$therapy{$line[0]}},'突变' if !(grep{$_ eq '突变'}@{$therapy{$line[0]}});;
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my @line = split("\t");
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if ($line[9] eq 'V' and $line[14] eq 'A' and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) and $line[0] !~ /,/) {
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push @{$cancer{$line[0]}}, $dis{lc $line[2]} if !(grep {$_ eq $dis{lc $line[2]}} @{$cancer{$line[0]}});
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if ($line[1] =~ /fusion/i) {
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push @{$therapy{$line[0]}}, '融合' if !(grep {$_ eq '融合'} @{$therapy{$line[0]}});
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}
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elsif ($line[1] eq "Deletion" or $line[1] =~ /Amplification/) {
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push @{$therapy{$line[0]}}, '扩增' if !(grep {$_ eq '扩增'} @{$therapy{$line[0]}});
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}
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else {
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push @{$therapy{$line[0]}}, '突变' if !(grep {$_ eq '突变'} @{$therapy{$line[0]}});;
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}
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}
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}
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for my $gene(sort keys %therapy){
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print OUT "$gene\t",join("/",@{$therapy{$gene}}),"\t未检出变异\t",join("/",@{$cancer{$gene}}),"\n";
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for my $gene (sort keys %therapy) {
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print OUT "$gene\t", join("/", @{$therapy{$gene}}), "\t未检出变异\t", join("/", @{$cancer{$gene}}), "\n";
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}
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@ -0,0 +1,287 @@
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#!/usr/bin/env python3
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import argparse
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import os
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import pandas as pd
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def single_monitoring(name, vcf, bed, freq_range, output_dir):
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vcf_header = [] # 用于存储VCF文件头部分
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vcf_data = [] # 用于存储筛选后的VCF数据
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p_value_list = [] # 用于存储符合条件的 p-value
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# 按行处理，保存为列表
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with open(vcf, 'r') as vcf_file:
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for line in vcf_file:
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if line.startswith("#"):
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vcf_header.append(line)
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else:
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vcf_data.append(line)
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# bed 处理
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df_position = pd.read_csv(bed, sep='\t', header=None, names=range(4))
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position_list = list(df_position[2])
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chr_list = list(df_position[0])
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result_data = []
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for i in range(len(position_list)):
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filtered_lines = [line for line in vcf_data if
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line.split()[1] == str(position_list[i]) and line.split()[0] == str(chr_list[i]) and len(
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line.split()[3]) < 2 and len(line.split()[4]) < 2]
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for line in filtered_lines:
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p_value_str = line.split()[9].split(":")[4]
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p_value = float(p_value_str[:-1]) / 100 if p_value_str[-1] == "%" else float(p_value_str)
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if 0.1 <= p_value <= 0.9:
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result_data.append(line)
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p_value_list.append(p_value)
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select_vcf = os.path.join(output_dir, f'{name}_select.vcf')
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with open(select_vcf, 'w') as output:
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for header_line in vcf_header:
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output.write(header_line)
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for data_line in result_data:
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output.write(data_line)
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count_normal = 0
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count_exception = 0
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for p_value in p_value_list:
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if freq_range[0] <= p_value <= freq_range[1]:
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count_normal += 1
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else:
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count_exception += 1
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count_all = count_exception + count_normal
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if count_all == 0:
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z_score = 0
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else:
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z_score = count_exception / count_all
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res = dict(
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barcode=name,
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count_normal=count_normal,
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count_exception=count_exception,
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z_score=z_score
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)
|
||||
pd.DataFrame([res]).to_csv(os.path.join(f'{name}_pollution.csv'), sep="\t", index=False)
|
||||
|
||||
|
||||
# 根据小bed筛选vcf
|
||||
def select_position(vcf, bed, matched_file, unmatched_file):
|
||||
vcf_header = [] # 用于存储VCF文件头部分
|
||||
vcf_data = [] # 用于存储筛选后的VCF数据
|
||||
|
||||
# 按行处理，保存为列表
|
||||
with open(vcf, 'r') as vcf_file:
|
||||
for line in vcf_file:
|
||||
if line.startswith("#"):
|
||||
vcf_header.append(line)
|
||||
else:
|
||||
vcf_data.append(line)
|
||||
|
||||
df_position = pd.read_csv(bed, sep='\t', header=None, names=range(4))
|
||||
position_list = list(df_position[2])
|
||||
chr_list = list(df_position[0])
|
||||
result_data = []
|
||||
unmatched_data = [] # 用于存储未匹配的数据
|
||||
|
||||
for i in range(len(position_list)):
|
||||
filtered_lines = [line for line in vcf_data if
|
||||
line.split()[1] == str(position_list[i]) and line.split()[0] == str(chr_list[i]) and len(
|
||||
line.split()[3]) < 2 and len(line.split()[4]) < 2]
|
||||
if not filtered_lines: # 如果没有匹配的点，添加到未匹配数据列表
|
||||
unmatched_data.append(f"{chr_list[i]}\t{position_list[i]}\t.\t.\t.\t.\t.\n")
|
||||
result_data.extend(filtered_lines)
|
||||
|
||||
with open(matched_file, 'w') as output:
|
||||
for header_line in vcf_header:
|
||||
output.write(header_line)
|
||||
for data_line in result_data:
|
||||
output.write(data_line)
|
||||
|
||||
with open(unmatched_file, 'w') as unmatched_output:
|
||||
unmatched_output.writelines(unmatched_data)
|
||||
|
||||
return matched_file, unmatched_file
|
||||
|
||||
|
||||
# 处理体系、胚系的vcf，得到目标信息
|
||||
def process_judge_vcf(input_vcf, output_vcf):
|
||||
with open(input_vcf, 'r') as input_file, open(output_vcf, 'w') as output_file:
|
||||
for line in input_file:
|
||||
if not line.startswith("#"):
|
||||
fields = line.strip().split('\t')
|
||||
info = fields[9].split(":")
|
||||
percentage = float(info[4])
|
||||
|
||||
if 0.1 <= percentage <= 0.9:
|
||||
b = 0.5
|
||||
elif percentage < 0.1:
|
||||
b = 0
|
||||
elif percentage > 0.9:
|
||||
b = 1
|
||||
|
||||
# 构建新的行数据
|
||||
new_line = '\t'.join([fields[0], fields[1], fields[3], fields[4], info[4], str(b), info[2]])
|
||||
output_file.write(new_line + '\n')
|
||||
return output_vcf
|
||||
|
||||
|
||||
def merge_and_sort_files(matched_file, unmatched_file, output_file):
|
||||
# 检查 unmatched_file 是否为空
|
||||
if os.stat(unmatched_file).st_size == 0:
|
||||
# 对 matched_file 进行排序并写入 output_file
|
||||
matched_df = pd.read_csv(matched_file, sep='\t', header=None)
|
||||
sorted_df = matched_df.sort_values(by=[0, 1])
|
||||
sorted_df.to_csv(output_file, sep='\t', header=False, index=False)
|
||||
return output_file
|
||||
|
||||
# 如果 unmatched_file 不为空，继续合并和排序操作
|
||||
matched_df = pd.read_csv(matched_file, sep='\t', header=None)
|
||||
unmatched_df = pd.read_csv(unmatched_file, sep='\t', header=None)
|
||||
|
||||
# 合并数据帧
|
||||
combined_df = pd.concat([matched_df, unmatched_df])
|
||||
|
||||
# 根据第一列和第二列排序
|
||||
sorted_df = combined_df.sort_values(by=[0, 1])
|
||||
|
||||
# 将排序后的数据写入输出文件
|
||||
sorted_df.to_csv(output_file, sep='\t', header=False, index=False)
|
||||
return output_file
|
||||
|
||||
|
||||
# 合并体系，胚系
|
||||
def merge_and_compare_files(somatic_file, germline_file, output_merged_file, output_final_file):
|
||||
# 合并两个文件
|
||||
with open(somatic_file, 'r') as somatic, open(germline_file, 'r') as germline:
|
||||
merged_lines = [f"{somatic_line.strip()}\t{germline_line.strip()}" for somatic_line, germline_line in
|
||||
zip(somatic, germline)]
|
||||
|
||||
# 将合并后的数据写入输出文件
|
||||
with open(output_merged_file, 'w') as output_file:
|
||||
output_file.write('\n'.join(merged_lines))
|
||||
|
||||
# 比较两列数据并添加比较结果列
|
||||
with open(output_merged_file, 'r') as merged, open(output_final_file, 'w') as final_output:
|
||||
for line in merged:
|
||||
fields = line.strip().split('\t')
|
||||
if fields[5] == fields[12]:
|
||||
comparison_result = "yes"
|
||||
else:
|
||||
comparison_result = "no"
|
||||
final_output.write(f"{line.strip()}\t{comparison_result}\n")
|
||||
return output_merged_file, output_final_file
|
||||
|
||||
|
||||
# 根据大bed筛选vcf，作cnvkit的图
|
||||
def select_cnvkit_vcf(vcf, bed, output_file):
|
||||
vcf_header = [] # 用于存储VCF文件头部分
|
||||
vcf_data = [] # 用于存储筛选后的VCF数据
|
||||
p_value_list = [] # 用于存储符合条件的 p-value
|
||||
|
||||
# 按行处理，保存为列表
|
||||
with open(vcf, 'r') as vcf_file:
|
||||
for line in vcf_file:
|
||||
if line.startswith("#"):
|
||||
vcf_header.append(line)
|
||||
else:
|
||||
vcf_data.append(line)
|
||||
|
||||
df_position = pd.read_csv(bed, sep='\t', header=None, names=range(4))
|
||||
position_list = list(df_position[2])
|
||||
chr_list = list(df_position[0])
|
||||
result_data = []
|
||||
for i in range(len(position_list)):
|
||||
filtered_lines = [line for line in vcf_data if
|
||||
line.split()[1] == str(position_list[i]) and line.split()[0] == str(chr_list[i]) and len(
|
||||
line.split()[3]) < 2 and len(line.split()[4]) < 2]
|
||||
for line in filtered_lines:
|
||||
p_value_str = line.split()[9].split(":")[4]
|
||||
p_value = float(p_value_str[:-1]) / 100 if p_value_str[-1] == "%" else float(p_value_str)
|
||||
if 0.1 <= p_value <= 0.9:
|
||||
result_data.append(line)
|
||||
|
||||
with open(output_file, 'w') as output:
|
||||
for header_line in vcf_header:
|
||||
output.write(header_line)
|
||||
for data_line in result_data:
|
||||
output.write(data_line)
|
||||
|
||||
return output_file
|
||||
|
||||
|
||||
def paired_monitoring(name, somatic_vcf, germline_vcf, ref_bed, cnvkit_ref_bed, output_dir):
|
||||
# 处理体系，根据bed筛选
|
||||
select_position_output_file1 = os.path.join(output_dir, f'{name}_somatic_matched.vcf')
|
||||
select_position_output_file2 = os.path.join(output_dir, f'{name}_somatic_unmatched.vcf')
|
||||
somatic_matched_file, somatic_unmatched_file = select_position(somatic_vcf, ref_bed, select_position_output_file1,
|
||||
select_position_output_file2)
|
||||
# 处理胚系，根据bed筛选
|
||||
select_position_output_file3 = os.path.join(output_dir, f'{name}_germline_matched.vcf')
|
||||
select_position_output_file4 = os.path.join(output_dir, f'{name}_germline_unmatched.vcf')
|
||||
Germline_matched_file, Germline_unmatched_file = select_position(germline_vcf, ref_bed,
|
||||
select_position_output_file3,
|
||||
select_position_output_file4)
|
||||
# 处理体系，数值转换
|
||||
process_judge_vcf_file1 = os.path.join(output_dir, f'{name}_somatic_matched_add_judge.vcf')
|
||||
somatic_matched_add_judge_file = process_judge_vcf(somatic_matched_file, process_judge_vcf_file1)
|
||||
# 处理胚系，数值转换
|
||||
process_judge_vcf_file2 = os.path.join(output_dir, f'{name}_germline_matched_add_judge.vcf')
|
||||
germline_matched_add_judge_file = process_judge_vcf(Germline_matched_file, process_judge_vcf_file2)
|
||||
# 合并体系，将匹配到的和未匹配到bed的的合并
|
||||
merge_and_sort_files_file1 = os.path.join(output_dir, f'{name}_somatic_merged.vcf')
|
||||
somatic_merged_file = merge_and_sort_files(somatic_matched_add_judge_file, somatic_unmatched_file,
|
||||
merge_and_sort_files_file1)
|
||||
# 合并胚系，将匹配到的和未匹配到bed的的合并
|
||||
merge_and_sort_files_file2 = os.path.join(output_dir, f'{name}_germline__merged.vcf')
|
||||
Germline_merged_file = merge_and_sort_files(germline_matched_add_judge_file, Germline_unmatched_file,
|
||||
merge_and_sort_files_file2)
|
||||
# 合并胚系，体系，将体系，胚系两个合并文件再合并
|
||||
result_pro_file = os.path.join(output_dir, f'{name}_result_pro.txt')
|
||||
result_file = os.path.join(output_dir, f'{name}_contaminate_result.txt')
|
||||
merge_and_compare_files(somatic_merged_file, Germline_merged_file, result_pro_file, result_file)
|
||||
##筛选作图vcf
|
||||
cnvkit_output_file = os.path.join(output_dir, f'{name}_select_cnvkit.vcf')
|
||||
select_cnvkit_vcf(germline_vcf, cnvkit_ref_bed, cnvkit_output_file)
|
||||
##删除中间文件
|
||||
os.remove(select_position_output_file1)
|
||||
os.remove(select_position_output_file2)
|
||||
os.remove(select_position_output_file3)
|
||||
os.remove(select_position_output_file4)
|
||||
os.remove(process_judge_vcf_file1)
|
||||
os.remove(process_judge_vcf_file2)
|
||||
os.remove(merge_and_sort_files_file1)
|
||||
os.remove(merge_and_sort_files_file2)
|
||||
os.remove(result_pro_file)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = argparse.ArgumentParser(description="Pollution Process Script")
|
||||
|
||||
parser.add_argument('-n', '--name', help="Name for sample", required=True)
|
||||
parser.add_argument('-b', '--ref_bed', help="ref_bed", required=True)
|
||||
parser.add_argument('-v', '--vcf', help="raw vcf for prbe 160 or 17 ; somatic vcf for prbe 682 or 624",
|
||||
required=True)
|
||||
parser.add_argument('-v2', '--vcf2', help="germline vcf; required when prbe 682 or 624")
|
||||
parser.add_argument('-c', '--cnvkit_bed', help="cnvkit_bed; required when prbe 682 or 624")
|
||||
parser.add_argument('-p', '--probe', help="probe, 682, 624, 160, 17 for now ", required=True)
|
||||
parser.add_argument('-o', '--output_dir', help="Output directory, default ./", default='')
|
||||
args = parser.parse_args()
|
||||
|
||||
bed_path = os.path.realpath(args.ref_bed)
|
||||
print(f'污染检测使用ref_bed: {bed_path}')
|
||||
probe = args.probe
|
||||
|
||||
if probe == '160' or probe == '17':
|
||||
freq_range = {"17": [0.3452, 0.6512], "160": [0.2930, 0.6753]}.get(probe)
|
||||
single_monitoring(args.name, args.vcf, bed_path, freq_range, args.output_dir)
|
||||
elif probe == '682' or probe == '624':
|
||||
if not args.vcf2:
|
||||
parser.error('--vcf2 is required in prbe 682 or 624')
|
||||
if not args.cnvkit_bed:
|
||||
parser.error('--cnvkit_bed is required in prbe 682 or 624')
|
||||
cnvkit_bed_path = os.path.realpath(args.cnvkit_bed)
|
||||
print(f'污染检测使用cnvkit_bed: {cnvkit_bed_path}')
|
||||
paired_monitoring(args.name, args.vcf, args.vcf2, bed_path, args.cnvkit_bed, args.output_dir)
|
||||
else:
|
||||
parser.error('probe error. 682, 624, 160, 17 for now')
|
||||
|
||||
|
|
@ -17,7 +17,9 @@ def database():
|
|||
增持匹配信息
|
||||
"""
|
||||
|
||||
path = os.environ.get('DATABASE', '/home/zhangchao/project/pipeline/workflow/database/')
|
||||
path = os.environ.get('DATABASE')
|
||||
if not path:
|
||||
raise UserWarning('未设置DATABASE环境变量')
|
||||
# gene function 基因功能描述信息
|
||||
gene_function_path = os.path.join(path, 'gene_function.txt')
|
||||
gene_function_df = pd.read_csv(gene_function_path, sep='\t')
|
||||
|
|
|
|||
|
|
@ -0,0 +1,634 @@
|
|||
chr5 224633 224633
|
||||
chr5 226160 226160
|
||||
chr5 228362 228362
|
||||
chr5 230980 230980
|
||||
chr5 231111 231111
|
||||
chr5 231143 231143
|
||||
chr5 233734 233734
|
||||
chr5 251784 251784
|
||||
chr5 256451 256451
|
||||
chr5 256472 256472
|
||||
chr11 534242 534242
|
||||
chr18 673447 673447
|
||||
chr18 673449 673449
|
||||
chr19 1208289 1208289
|
||||
chr19 1220321 1220321
|
||||
chr19 1221161 1221161
|
||||
chr19 1222012 1222012
|
||||
chr4 1801064 1801064
|
||||
chr4 1805478 1805478
|
||||
chr4 1806519 1806519
|
||||
chr4 1807894 1807894
|
||||
chr16 2103408 2103408
|
||||
chr16 2120402 2120402
|
||||
chr16 2138219 2138219
|
||||
chr19 3110349 3110349
|
||||
chr19 3113305 3113305
|
||||
chr19 3114954 3114954
|
||||
chr19 3115124 3115124
|
||||
chr19 3119184 3119184
|
||||
chr19 3119239 3119239
|
||||
chr11 4104007 4104007
|
||||
chr11 4104060 4104060
|
||||
chr11 4104087 4104087
|
||||
chr11 4113395 4113395
|
||||
chr11 4113470 4113470
|
||||
chr11 4113471 4113471
|
||||
chr11 4115487 4115487
|
||||
chr11 4115541 4115541
|
||||
chr11 4159457 4159457
|
||||
chr11 4159466 4159466
|
||||
chr12 4388084 4388084
|
||||
chr9 5050706 5050706
|
||||
chr9 5078291 5078291
|
||||
chr9 5081780 5081780
|
||||
chr9 5090810 5090810
|
||||
chr9 5090934 5090934
|
||||
chr9 5557672 5557672
|
||||
chr9 5557708 5557708
|
||||
chr7 6013049 6013049
|
||||
chr7 6022626 6022626
|
||||
chr7 6022629 6022629
|
||||
chr7 6026384 6026384
|
||||
chr7 6026775 6026775
|
||||
chr7 6026942 6026942
|
||||
chr7 6026988 6026988
|
||||
chr7 6031102 6031102
|
||||
chr7 6036980 6036980
|
||||
chr7 6038722 6038722
|
||||
chr7 6043386 6043386
|
||||
chr7 6045627 6045627
|
||||
chr17 7578645 7578645
|
||||
chr17 7579472 7579472
|
||||
chr5 7870973 7870973
|
||||
chr10 8111409 8111409
|
||||
chr1 11174331 11174331
|
||||
chr1 11174851 11174851
|
||||
chr1 11181327 11181327
|
||||
chr1 11181457 11181457
|
||||
chr1 11190646 11190646
|
||||
chr1 11190730 11190730
|
||||
chr1 11199518 11199518
|
||||
chr1 11199541 11199541
|
||||
chr1 11205058 11205058
|
||||
chr1 11272468 11272468
|
||||
chr1 11288758 11288758
|
||||
chr1 11300338 11300338
|
||||
chr1 11301714 11301714
|
||||
chr1 11303153 11303153
|
||||
chr1 11303383 11303383
|
||||
chr1 11854457 11854457
|
||||
chr1 11854476 11854476
|
||||
chr1 11856378 11856378
|
||||
chr3 14187449 14187449
|
||||
chr1 17380497 17380497
|
||||
chr2 17938501 17938501
|
||||
chr19 17942005 17942005
|
||||
chr19 17946054 17946054
|
||||
chr19 17952609 17952609
|
||||
chr19 17953321 17953321
|
||||
chr19 17955021 17955021
|
||||
chr1 20915507 20915507
|
||||
chr1 20915531 20915531
|
||||
chr1 20915590 20915590
|
||||
chr1 20915701 20915701
|
||||
chr12 21331599 21331599
|
||||
chr12 21331625 21331625
|
||||
chr9 21968199 21968199
|
||||
chr9 21968712 21968712
|
||||
chr12 25362777 25362777
|
||||
chr12 25368462 25368462
|
||||
chr2 25469502 25469502
|
||||
chr2 25536827 25536827
|
||||
chr4 25666099 25666099
|
||||
chr1 27089690 27089690
|
||||
chr13 28592546 28592546
|
||||
chr13 28608459 28608459
|
||||
chr13 28609825 28609825
|
||||
chr13 28610183 28610183
|
||||
chr13 28622544 28622544
|
||||
chr13 28623699 28623699
|
||||
chr13 28623759 28623759
|
||||
chr13 28624294 28624294
|
||||
chr13 28636084 28636084
|
||||
chr13 28674628 28674628
|
||||
chr22 29104955 29104955
|
||||
chr22 29104959 29104959
|
||||
chr22 29130458 29130458
|
||||
chr2 29416366 29416366
|
||||
chr2 29416481 29416481
|
||||
chr2 29416572 29416572
|
||||
chr2 29420550 29420550
|
||||
chr2 29443617 29443617
|
||||
chr2 29443749 29443749
|
||||
chr2 29444076 29444076
|
||||
chr2 29444095 29444095
|
||||
chr2 29445458 29445458
|
||||
chr2 29445602 29445602
|
||||
chr2 29446178 29446178
|
||||
chr2 29446184 29446184
|
||||
chr2 29446701 29446701
|
||||
chr2 29446721 29446721
|
||||
chr2 29446880 29446880
|
||||
chr2 29447108 29447108
|
||||
chr2 29447253 29447253
|
||||
chr2 29448760 29448760
|
||||
chr2 29449005 29449005
|
||||
chr2 29449526 29449526
|
||||
chr2 29449819 29449819
|
||||
chr2 29455267 29455267
|
||||
chr17 29508775 29508775
|
||||
chr17 29541437 29541437
|
||||
chr2 29543663 29543663
|
||||
chr17 29553485 29553485
|
||||
chr17 29653293 29653293
|
||||
chr17 29663624 29663624
|
||||
chr17 29663625 29663625
|
||||
chr17 29670190 29670190
|
||||
chr17 29679246 29679246
|
||||
chr17 29686024 29686024
|
||||
chr17 29705947 29705947
|
||||
chr2 29940529 29940529
|
||||
chr2 30143499 30143499
|
||||
chr6 32782149 32782149
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||||
chr1 156844979 156844979
|
||||
chr1 156845095 156845095
|
||||
chr1 156845848 156845848
|
||||
chr1 156846233 156846233
|
||||
chr1 156848995 156848995
|
||||
chr1 156849780 156849780
|
||||
chr6 159189454 159189454
|
||||
chr6 159190019 159190019
|
||||
chr6 159190184 159190184
|
||||
chr6 159191788 159191788
|
||||
chr6 160113872 160113872
|
||||
chr1 162737116 162737116
|
||||
chr1 162740327 162740327
|
||||
chr1 162743418 162743418
|
||||
chr3 178922274 178922274
|
||||
chr3 178938747 178938747
|
||||
chr3 178942431 178942431
|
||||
chr1 204501383 204501383
|
||||
chr1 204512100 204512100
|
||||
chr1 204516025 204516025
|
||||
chr2 212251864 212251864
|
||||
chr2 212652698 212652698
|
||||
chr2 215593233 215593233
|
||||
chr2 215595645 215595645
|
||||
chr2 215632192 215632192
|
||||
chr2 215632255 215632255
|
||||
chr2 215632256 215632256
|
||||
chr2 215634055 215634055
|
||||
chr2 215645464 215645464
|
||||
chr2 215645545 215645545
|
||||
chr2 215674224 215674224
|
||||
chr2 215674323 215674323
|
||||
chr2 216212339 216212339
|
||||
chr2 234669144 234669144
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,128 @@
|
|||
chr1 2488153 2488153
|
||||
chr1 23885599 23885599
|
||||
chr1 65321388 65321388
|
||||
chr1 120612006 120612006
|
||||
chr1 193094375 193094375
|
||||
chr1 226570840 226570840
|
||||
chr2 47693959 47693959
|
||||
chr2 48030838 48030838
|
||||
chr2 61749716 61749716
|
||||
chr2 141032088 141032088
|
||||
chr2 215645464 215645464
|
||||
chr3 30686414 30686414
|
||||
chr3 47125385 47125385
|
||||
chr3 134644636 134644636
|
||||
chr3 142281612 142281612
|
||||
chr3 192053274 192053274
|
||||
chr4 55599436 55599436
|
||||
chr4 143007419 143007419
|
||||
chr4 153252061 153252061
|
||||
chr4 185310218 185310218
|
||||
chr4 25666099 25666099
|
||||
chr5 35857177 35857177
|
||||
chr5 38955796 38955796
|
||||
chr5 39074296 39074296
|
||||
chr5 67522722 67522722
|
||||
chr5 112162854 112162854
|
||||
chr5 149435759 149435759
|
||||
chr5 161119125 161119125
|
||||
chr5 170819887 170819887
|
||||
chr5 180046344 180046344
|
||||
chr6 30858857 30858857
|
||||
chr6 32797876 32797876
|
||||
chr6 36645696 36645696
|
||||
chr6 117678083 117678083
|
||||
chr6 117714346 117714346
|
||||
chr7 2946461 2946461
|
||||
chr7 2962753 2962753
|
||||
chr7 87138645 87138645
|
||||
chr7 151970931 151970931
|
||||
chr8 90955624 90955624
|
||||
chr8 90970935 90970935
|
||||
chr8 90995019 90995019
|
||||
chr8 68864728 68864728
|
||||
chr8 38322346 38322346
|
||||
chr8 145742879 145742879
|
||||
chr9 5081780 5081780
|
||||
chr9 8389364 8389364
|
||||
chr9 93657761 93657761
|
||||
chr9 98209594 98209594
|
||||
chr9 21991923 21991923
|
||||
chr9 37020622 37020622
|
||||
chr9 21975017 21975017
|
||||
chr10 43600689 43600689
|
||||
chr10 89720907 89720907
|
||||
chr10 104596981 104596981
|
||||
chr10 104849468 104849468
|
||||
chr10 104855656 104855656
|
||||
chr10 123239112 123239112
|
||||
chr11 32410774 32410774
|
||||
chr11 69462910 69462910
|
||||
chr11 94197260 94197260
|
||||
chr11 94225807 94225807
|
||||
chr11 94225920 94225920
|
||||
chr11 125497466 125497466
|
||||
chr12 1040373 1040373
|
||||
chr12 4553383 4553383
|
||||
chr12 6711147 6711147
|
||||
chr12 21331625 21331625
|
||||
chr12 49427652 49427652
|
||||
chr12 49444545 49444545
|
||||
chr12 121416622 121416622
|
||||
chr12 133202215 133202215
|
||||
chr13 21562948 21562948
|
||||
chr13 28609825 28609825
|
||||
chr13 32936646 32936646
|
||||
chr13 113889474 113889474
|
||||
chr13 113907391 113907391
|
||||
chr14 105239894 105239894
|
||||
chr14 105246325 105246325
|
||||
chr14 38064215 38064215
|
||||
chr14 20820537 20820537
|
||||
chr14 35871217 35871217
|
||||
chr15 41865488 41865488
|
||||
chr15 51502986 51502986
|
||||
chr15 51529112 51529112
|
||||
chr15 99456253 99456253
|
||||
chr15 99478225 99478225
|
||||
chr15 51558731 51558731
|
||||
chr16 68857441 68857441
|
||||
chr16 359953 359953
|
||||
chr16 89805977 89805977
|
||||
chr16 89838078 89838078
|
||||
chr16 89857964 89857964
|
||||
chr17 7983969 7983969
|
||||
chr17 29486152 29486152
|
||||
chr17 29508775 29508775
|
||||
chr17 29546175 29546175
|
||||
chr17 29559932 29559932
|
||||
chr17 29653293 29653293
|
||||
chr17 37879762 37879762
|
||||
chr17 62007498 62007498
|
||||
chr17 78919558 78919558
|
||||
chr19 3110349 3110349
|
||||
chr19 3119239 3119239
|
||||
chr19 4101062 4101062
|
||||
chr19 11136215 11136215
|
||||
chr19 15289613 15289613
|
||||
chr19 15295134 15295134
|
||||
chr19 41725271 41725271
|
||||
chr20 43956527 43956527
|
||||
chr20 43956636 43956636
|
||||
chr20 43958850 43958850
|
||||
chr20 43958872 43958872
|
||||
chr20 54959296 54959296
|
||||
chr20 54961541 54961541
|
||||
chr21 37518706 37518706
|
||||
chr21 39752673 39752673
|
||||
chr21 39753375 39753375
|
||||
chr22 41568480 41568480
|
||||
chr22 30038152 30038152
|
||||
chr22 30079213 30079213
|
||||
chrX 76937963 76937963
|
||||
chrX 39922359 39922359
|
||||
chrX 39932907 39932907
|
||||
chrX 44938563 44938563
|
||||
chrX 100608191 100608191
|
||||
chrX 100611285 100611285
|
||||
chrX 76940534 76940534
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,128 @@
|
|||
chr1 2488153 2488153
|
||||
chr1 23885599 23885599
|
||||
chr1 65321388 65321388
|
||||
chr1 120612006 120612006
|
||||
chr1 193094375 193094375
|
||||
chr1 226570840 226570840
|
||||
chr2 47693959 47693959
|
||||
chr2 48030838 48030838
|
||||
chr2 61749716 61749716
|
||||
chr2 141032088 141032088
|
||||
chr2 215645464 215645464
|
||||
chr3 30686414 30686414
|
||||
chr3 47125385 47125385
|
||||
chr3 134644636 134644636
|
||||
chr3 142281612 142281612
|
||||
chr3 192053274 192053274
|
||||
chr4 55599436 55599436
|
||||
chr4 143007419 143007419
|
||||
chr4 153252061 153252061
|
||||
chr4 185310218 185310218
|
||||
chr4 25666099 25666099
|
||||
chr5 35857177 35857177
|
||||
chr5 38955796 38955796
|
||||
chr5 39074296 39074296
|
||||
chr5 67522722 67522722
|
||||
chr5 112162854 112162854
|
||||
chr5 149435759 149435759
|
||||
chr5 161119125 161119125
|
||||
chr5 170819887 170819887
|
||||
chr5 180046344 180046344
|
||||
chr6 30858857 30858857
|
||||
chr6 32797876 32797876
|
||||
chr6 36645696 36645696
|
||||
chr6 117678083 117678083
|
||||
chr6 117714346 117714346
|
||||
chr7 2946461 2946461
|
||||
chr7 2962753 2962753
|
||||
chr7 87138645 87138645
|
||||
chr7 151970931 151970931
|
||||
chr8 90955624 90955624
|
||||
chr8 90970935 90970935
|
||||
chr8 90995019 90995019
|
||||
chr8 68864728 68864728
|
||||
chr8 38322346 38322346
|
||||
chr8 145742879 145742879
|
||||
chr9 5081780 5081780
|
||||
chr9 8389364 8389364
|
||||
chr9 93657761 93657761
|
||||
chr9 98209594 98209594
|
||||
chr9 21991923 21991923
|
||||
chr9 37020622 37020622
|
||||
chr9 21975017 21975017
|
||||
chr10 43600689 43600689
|
||||
chr10 89720907 89720907
|
||||
chr10 104596981 104596981
|
||||
chr10 104849468 104849468
|
||||
chr10 104855656 104855656
|
||||
chr10 123239112 123239112
|
||||
chr11 32410774 32410774
|
||||
chr11 69462910 69462910
|
||||
chr11 94197260 94197260
|
||||
chr11 94225807 94225807
|
||||
chr11 94225920 94225920
|
||||
chr11 125497466 125497466
|
||||
chr12 1040373 1040373
|
||||
chr12 4553383 4553383
|
||||
chr12 6711147 6711147
|
||||
chr12 21331625 21331625
|
||||
chr12 49427652 49427652
|
||||
chr12 49444545 49444545
|
||||
chr12 121416622 121416622
|
||||
chr12 133202215 133202215
|
||||
chr13 21562948 21562948
|
||||
chr13 28609825 28609825
|
||||
chr13 32936646 32936646
|
||||
chr13 113889474 113889474
|
||||
chr13 113907391 113907391
|
||||
chr14 105239894 105239894
|
||||
chr14 105246325 105246325
|
||||
chr14 38064215 38064215
|
||||
chr14 20820537 20820537
|
||||
chr14 35871217 35871217
|
||||
chr15 41865488 41865488
|
||||
chr15 51502986 51502986
|
||||
chr15 51529112 51529112
|
||||
chr15 99456253 99456253
|
||||
chr15 99478225 99478225
|
||||
chr15 51558731 51558731
|
||||
chr16 68857441 68857441
|
||||
chr16 359953 359953
|
||||
chr16 89805977 89805977
|
||||
chr16 89838078 89838078
|
||||
chr16 89857964 89857964
|
||||
chr17 7983969 7983969
|
||||
chr17 29486152 29486152
|
||||
chr17 29508775 29508775
|
||||
chr17 29546175 29546175
|
||||
chr17 29559932 29559932
|
||||
chr17 29653293 29653293
|
||||
chr17 37879762 37879762
|
||||
chr17 62007498 62007498
|
||||
chr17 78919558 78919558
|
||||
chr19 3110349 3110349
|
||||
chr19 3119239 3119239
|
||||
chr19 4101062 4101062
|
||||
chr19 11136215 11136215
|
||||
chr19 15289613 15289613
|
||||
chr19 15295134 15295134
|
||||
chr19 41725271 41725271
|
||||
chr20 43956527 43956527
|
||||
chr20 43956636 43956636
|
||||
chr20 43958850 43958850
|
||||
chr20 43958872 43958872
|
||||
chr20 54959296 54959296
|
||||
chr20 54961541 54961541
|
||||
chr21 37518706 37518706
|
||||
chr21 39752673 39752673
|
||||
chr21 39753375 39753375
|
||||
chr22 41568480 41568480
|
||||
chr22 30038152 30038152
|
||||
chr22 30079213 30079213
|
||||
chrX 76937963 76937963
|
||||
chrX 39922359 39922359
|
||||
chrX 39932907 39932907
|
||||
chrX 44938563 44938563
|
||||
chrX 100608191 100608191
|
||||
chrX 100611285 100611285
|
||||
chrX 76940534 76940534
|
||||
|
|
@ -0,0 +1,128 @@
|
|||
chr1 2488153 2488153
|
||||
chr1 23885599 23885599
|
||||
chr1 65321388 65321388
|
||||
chr1 120612006 120612006
|
||||
chr1 193094375 193094375
|
||||
chr1 226570840 226570840
|
||||
chr2 47693959 47693959
|
||||
chr2 48030838 48030838
|
||||
chr2 61749716 61749716
|
||||
chr2 141032088 141032088
|
||||
chr2 215645464 215645464
|
||||
chr3 30686414 30686414
|
||||
chr3 47125385 47125385
|
||||
chr3 134644636 134644636
|
||||
chr3 142281612 142281612
|
||||
chr3 192053274 192053274
|
||||
chr4 55599436 55599436
|
||||
chr4 143007419 143007419
|
||||
chr4 153252061 153252061
|
||||
chr4 185310218 185310218
|
||||
chr4 25666099 25666099
|
||||
chr5 35857177 35857177
|
||||
chr5 38955796 38955796
|
||||
chr5 39074296 39074296
|
||||
chr5 67522722 67522722
|
||||
chr5 112162854 112162854
|
||||
chr5 149435759 149435759
|
||||
chr5 161119125 161119125
|
||||
chr5 170819887 170819887
|
||||
chr5 180046344 180046344
|
||||
chr6 30858857 30858857
|
||||
chr6 32797876 32797876
|
||||
chr6 36645696 36645696
|
||||
chr6 117678083 117678083
|
||||
chr6 117714346 117714346
|
||||
chr7 2946461 2946461
|
||||
chr7 2962753 2962753
|
||||
chr7 87138645 87138645
|
||||
chr7 151970931 151970931
|
||||
chr8 90955624 90955624
|
||||
chr8 90970935 90970935
|
||||
chr8 90995019 90995019
|
||||
chr8 68864728 68864728
|
||||
chr8 38322346 38322346
|
||||
chr8 145742879 145742879
|
||||
chr9 5081780 5081780
|
||||
chr9 8389364 8389364
|
||||
chr9 93657761 93657761
|
||||
chr9 98209594 98209594
|
||||
chr9 21991923 21991923
|
||||
chr9 37020622 37020622
|
||||
chr9 21975017 21975017
|
||||
chr10 43600689 43600689
|
||||
chr10 89720907 89720907
|
||||
chr10 104596981 104596981
|
||||
chr10 104849468 104849468
|
||||
chr10 104855656 104855656
|
||||
chr10 123239112 123239112
|
||||
chr11 32410774 32410774
|
||||
chr11 69462910 69462910
|
||||
chr11 94197260 94197260
|
||||
chr11 94225807 94225807
|
||||
chr11 94225920 94225920
|
||||
chr11 125497466 125497466
|
||||
chr12 1040373 1040373
|
||||
chr12 4553383 4553383
|
||||
chr12 6711147 6711147
|
||||
chr12 21331625 21331625
|
||||
chr12 49427652 49427652
|
||||
chr12 49444545 49444545
|
||||
chr12 121416622 121416622
|
||||
chr12 133202215 133202215
|
||||
chr13 21562948 21562948
|
||||
chr13 28609825 28609825
|
||||
chr13 32936646 32936646
|
||||
chr13 113889474 113889474
|
||||
chr13 113907391 113907391
|
||||
chr14 105239894 105239894
|
||||
chr14 105246325 105246325
|
||||
chr14 38064215 38064215
|
||||
chr14 20820537 20820537
|
||||
chr14 35871217 35871217
|
||||
chr15 41865488 41865488
|
||||
chr15 51502986 51502986
|
||||
chr15 51529112 51529112
|
||||
chr15 99456253 99456253
|
||||
chr15 99478225 99478225
|
||||
chr15 51558731 51558731
|
||||
chr16 68857441 68857441
|
||||
chr16 359953 359953
|
||||
chr16 89805977 89805977
|
||||
chr16 89838078 89838078
|
||||
chr16 89857964 89857964
|
||||
chr17 7983969 7983969
|
||||
chr17 29486152 29486152
|
||||
chr17 29508775 29508775
|
||||
chr17 29546175 29546175
|
||||
chr17 29559932 29559932
|
||||
chr17 29653293 29653293
|
||||
chr17 37879762 37879762
|
||||
chr17 62007498 62007498
|
||||
chr17 78919558 78919558
|
||||
chr19 3110349 3110349
|
||||
chr19 3119239 3119239
|
||||
chr19 4101062 4101062
|
||||
chr19 11136215 11136215
|
||||
chr19 15289613 15289613
|
||||
chr19 15295134 15295134
|
||||
chr19 41725271 41725271
|
||||
chr20 43956527 43956527
|
||||
chr20 43956636 43956636
|
||||
chr20 43958850 43958850
|
||||
chr20 43958872 43958872
|
||||
chr20 54959296 54959296
|
||||
chr20 54961541 54961541
|
||||
chr21 37518706 37518706
|
||||
chr21 39752673 39752673
|
||||
chr21 39753375 39753375
|
||||
chr22 41568480 41568480
|
||||
chr22 30038152 30038152
|
||||
chr22 30079213 30079213
|
||||
chrX 76937963 76937963
|
||||
chrX 39922359 39922359
|
||||
chrX 39932907 39932907
|
||||
chrX 44938563 44938563
|
||||
chrX 100608191 100608191
|
||||
chrX 100611285 100611285
|
||||
chrX 76940534 76940534
|
||||
|
|
@ -5,6 +5,15 @@ import os
|
|||
|
||||
run_wdl_path = os.path.join(os.path.dirname(__file__), 'run_wdl.py')
|
||||
|
||||
|
||||
def environ_test():
|
||||
workflow_path = os.environ.get('WORKFLOW', None)
|
||||
public_path = os.environ.get('PUBLIC', None)
|
||||
database_path = os.environ.get('DATABASE', None)
|
||||
if not (workflow_path and public_path and database_path):
|
||||
raise UserWarning('未设置WORKFLOW, PUBLIC, DATABASE环境')
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = argparse.ArgumentParser(description="JM to run pipeline")
|
||||
|
||||
|
|
@ -20,10 +29,13 @@ if __name__ == '__main__':
|
|||
parser.add_argument('-node', '--start_node',
|
||||
help="node begain to run; 'addQc', 'addAlignment', "
|
||||
"'addTarget', 'addFusion', 'addCnv', 'addMsi', 'addChemo',"
|
||||
" 'addHcs, addTmb, addAutoReport' and also run more than one node ,like this 'addTarget,addFusion'",
|
||||
" 'addHcs, addTmb, addAutoReport' and also run more than one "
|
||||
"node ,like this 'addTarget,addFusion'",
|
||||
default='addQc')
|
||||
args = parser.parse_args()
|
||||
|
||||
environ_test()
|
||||
|
||||
res_path = os.path.realpath(os.path.join(args.output_dir, args.barcode))
|
||||
|
||||
if not os.path.exists(res_path):
|
||||
|
|
@ -36,6 +48,6 @@ if __name__ == '__main__':
|
|||
f'-o {res_path} -b {args.probe} -p {args.project} -c {args.cancer} -w {args.wdl} ' \
|
||||
f'> {res_path}/{args.barcode}_run.log ' \
|
||||
f'2>> {res_path}/{args.barcode}_run.log &'
|
||||
with open(os.path.join(res_path, 'exec'), 'w') as execfile:
|
||||
execfile.write(cmd + '\n')
|
||||
# with open(os.path.join(res_path, 'exec'), 'w') as execfile:
|
||||
# execfile.write(cmd + '\n')
|
||||
os.system(cmd)
|
||||
|
|
|
|||
|
|
@ -39,7 +39,7 @@ def get_catecode(project, start_node='addQc'):
|
|||
}
|
||||
|
||||
runcode = get_branch_nodes(dag, start_node)
|
||||
public = os.environ.get('PUBLIC', '/home/zhangchao/project/pipeline/workflow/script/public')
|
||||
public = os.environ.get('DATABASE')
|
||||
path = os.path.join(public, 'info.csv')
|
||||
info = pd.read_csv(path)
|
||||
project = info[info['project'] == project]['CateCode']
|
||||
|
|
@ -83,15 +83,16 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
|
|||
jsfile.write(json.dumps(arg, indent=4, ensure_ascii=False))
|
||||
|
||||
# run pipeline
|
||||
cmd1 = 'export PATH=/home/zhangchao/project/pipeline/workflow/script:$PATH'
|
||||
cmd2 = 'export PUBLIC=/home/zhangchao/project/pipeline/workflow/script/public'
|
||||
# cmd1 = 'export PATH=/home/zhangchao/project/pipeline/workflow/script:$PATH'
|
||||
# cmd2 = 'export PUBLIC=/home/zhangchao/project/pipeline/workflow/script/public'
|
||||
cmd3 = f'cd {output_dir}'
|
||||
|
||||
# f'{"-Dcall-caching.enabled=false " if uncache else ""}'
|
||||
# f'-Dconfig.file=/home/zhangchao/project/pipeline/workflow/script/cromwell.examples.conf ' \
|
||||
|
||||
cmd4 = f'/usr/bin/java -jar /home/zhangchao/project/pipeline/workflow/software/cromwell-51.jar run --inputs {jsfile_path} {wdl}'
|
||||
cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}'
|
||||
cmd4 = f'/usr/bin/java -jar $WORKFLOW/software/cromwell-51.jar run --inputs {jsfile_path} {wdl}'
|
||||
# cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}'
|
||||
cmd = f'{cmd3}; {cmd4}'
|
||||
|
||||
# 记录开始时间
|
||||
start_time = time.time()
|
||||
|
|
@ -128,7 +129,8 @@ if __name__ == '__main__':
|
|||
parser.add_argument('-node', '--start_node',
|
||||
help="node begain to run; 'addQc', 'addAlignment', "
|
||||
"'addTarget', 'addFusion', 'addCnv', 'addMsi', 'addChemo',"
|
||||
" 'addHcs, 'addTmb', addAutoReport' and also run more than one node ,like this 'addTarget,addFusion'",
|
||||
" 'addHcs, 'addTmb', addAutoReport' and also run more than one node ,"
|
||||
"like this 'addTarget,addFusion'",
|
||||
default='addQc')
|
||||
args = parser.parse_args()
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,13 @@
|
|||
# 目录环境
|
||||
export WORKFLOW=/home/zhangchao/project/pipeline/workflow
|
||||
export PUBLIC=$WORKFLOW/script/public
|
||||
export DATABASE=$WORKFLOW/database
|
||||
|
||||
# python
|
||||
export PATH=/dataseq/product/workflow/software/Python-3.8.11/bin:$PATH
|
||||
|
||||
# script
|
||||
export PATH=$WORKFLOW/script:$PATH
|
||||
|
||||
# software
|
||||
export PATH=$WORKFLOW/software/bin:$PATH
|
||||
|
|
@ -9,7 +9,7 @@ my ($input, $output, $cancer_type) = @ARGV;
|
|||
my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
|
||||
print "Cnv药物注释使用路径：$database_path\n";
|
||||
|
||||
open THERAPY, "/dataseq/jmdna/codes/reportbase/targetTherapy.txt";
|
||||
open THERAPY, "$database_path/targetTherapy.txt";
|
||||
my $h1 = <THERAPY>;
|
||||
chomp $h1;
|
||||
my %therapy;
|
||||
|
|
@ -21,7 +21,7 @@ while (<THERAPY>) {
|
|||
|
||||
|
||||
##药物翻译信息
|
||||
open DRUG, "/dataseq/jmdna/codes/reportbase/target_drug.txt";
|
||||
open DRUG, "$database_path/target_drug.txt";
|
||||
my %drug;
|
||||
<DRUG>;
|
||||
while (<DRUG>) {
|
||||
|
|
@ -55,7 +55,7 @@ sub drug {
|
|||
}
|
||||
|
||||
|
||||
open DIS, "/dataseq/jmdna/codes/reportbase/oncotree.cancertype.20230801.txt";
|
||||
open DIS, "$database_path/oncotree.cancertype.20230801.txt";
|
||||
<DIS>;
|
||||
my (%dis, @id, %dis2);
|
||||
while (<DIS>) {
|
||||
|
|
|
|||
|
|
@ -114,7 +114,7 @@ while (<IN>) {
|
|||
($codon =~ /dup/) ? ("Exon $exon insertion") :
|
||||
("Exon $exon mutation");
|
||||
}
|
||||
elsif ($record{'AAChange_refGene'} =~ /splicing/) {
|
||||
elsif ($record{'Func_refGene'} =~ /splicing/) {
|
||||
$protein = 'Truncating Mutations';
|
||||
$mut_type = '';
|
||||
}
|
||||
|
|
@ -123,7 +123,7 @@ while (<IN>) {
|
|||
$mut_type = '';
|
||||
}
|
||||
else {
|
||||
print $_;
|
||||
print "药物注释未匹配到正确的protein或者mut_type";
|
||||
}
|
||||
|
||||
##若突变不存在于%mut,写入@vus,若突变存在于%mut且neutral，写入@neg;若基因不存在于%therapy，写入@vus;
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ task run_chemo {
|
|||
if [ ! -d ${output_dir}/chemo ];then
|
||||
mkdir ${output_dir}/chemo
|
||||
fi
|
||||
chemo.py -probe ${probe} -n ${name} -v ${vcf} -o ${output_dir}/chemo -c ${cancer} -p ${project}
|
||||
chemo.py -d $DATABASE/chemo_database.xlsx -probe ${probe} -n ${name} -v ${vcf} -o ${output_dir}/chemo -c ${cancer} -p ${project}
|
||||
>>>
|
||||
|
||||
output {
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ task run_hereditary {
|
|||
if [ ! -d ${output_dir}/hereditary ];then
|
||||
mkdir ${output_dir}/hereditary
|
||||
fi
|
||||
hereditary.py -p ${project} -n ${name} -f ${filter_txt} -o ${output_dir}/hereditary
|
||||
hereditary.py -d $DATABASE/hereditary_database.xlsx -p ${project} -n ${name} -f ${filter_txt} -o ${output_dir}/hereditary
|
||||
>>>
|
||||
|
||||
output {
|
||||
|
|
|
|||
|
|
@ -0,0 +1,65 @@
|
|||
task run_pollution {
|
||||
String name
|
||||
String output_dir
|
||||
String probe
|
||||
String vcf
|
||||
String? vcf2
|
||||
|
||||
command <<<
|
||||
|
||||
if [ ! -d ${output_dir}/pollution ];then
|
||||
mkdir ${output_dir}/pollution
|
||||
fi
|
||||
pollution.py -n ${name} \
|
||||
-v ${vcf} \
|
||||
-v2 ${vcf2} \
|
||||
-o ${output_dir}/pollution \
|
||||
-p ${probe} \
|
||||
-b $PUBLIC/pollution/${probe}_contaminate_ref.bed \
|
||||
-c $PUBLIC/pollution/${probe}_contaminate_cnvkit.bed
|
||||
>>>
|
||||
|
||||
output {
|
||||
String pollution_res = "${output_dir}/pollution/${name}_pollution.csv"
|
||||
}
|
||||
}
|
||||
|
||||
workflow call_pollution {
|
||||
|
||||
Boolean run=true
|
||||
|
||||
String tumor
|
||||
String? normal
|
||||
String output_dir
|
||||
String probe
|
||||
String raw_vcf
|
||||
String somatic_vcf
|
||||
String germline_vcf
|
||||
|
||||
if (run) {
|
||||
if (defined(normal)) {
|
||||
call run_pollution as run_pollution_paired {
|
||||
input:
|
||||
name=tumor,
|
||||
output_dir=output_dir,
|
||||
probe=probe,
|
||||
vcf=somatic_vcf,
|
||||
vcf2=germline_vcf
|
||||
}
|
||||
}
|
||||
|
||||
if (!defined(normal)) {
|
||||
call run_pollution as run_pollution_single {
|
||||
input:
|
||||
name=tumor,
|
||||
output_dir=output_dir,
|
||||
probe=probe,
|
||||
vcf=raw_vcf
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
output {
|
||||
String pollution_res = "${output_dir}/pollution/${name}_pollution.csv"
|
||||
}
|
||||
}
|
||||
|
|
@ -33,6 +33,7 @@ workflow call_postprocess {
|
|||
String? cnv
|
||||
String? msi
|
||||
String? hereditary
|
||||
String? pollution
|
||||
String? chemo
|
||||
String name
|
||||
String? normal
|
||||
|
|
@ -48,9 +49,9 @@ workflow call_postprocess {
|
|||
msi=msi,
|
||||
hereditary=hereditary,
|
||||
chemo=chemo,
|
||||
pollution=pollution,
|
||||
name=name,
|
||||
normal=normal,
|
||||
normal=normal,
|
||||
output_dir=output_dir,
|
||||
cancer=cancer
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue