From b9685fd29e10f928c193d7dacb70eee5d444b7b8 Mon Sep 17 00:00:00 2001 From: chaopower Date: Thu, 30 Nov 2023 15:31:35 +0800 Subject: [PATCH] =?UTF-8?q?=E6=B7=BB=E5=8A=A0pollution?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- database/chemo_database.xlsx | Bin 0 -> 83133 bytes database/hereditary_database.xlsx | Bin 0 -> 75813 bytes database/info.csv | 80 +- pipeline.wdl | 21 +- script/chemo.py | 3 +- script/filter_cnv.pl | 9 +- script/filter_fusion.pl | 4 +- script/filter_longindel.pl | 9 +- script/filter_promoter.pl | 52 + script/filter_snpindel.pl | 2 +- script/hereditary.py | 3 +- script/indication.pl | 88 +- script/pollution.py | 287 + script/postprocess.py | 4 +- .../public/pollution/160_contaminate_ref.bed | 634 +++ .../public/pollution/17_contaminate_ref.bed | 4835 +++++++++++++++++ .../pollution/624_contaminate_cnvkit.bed | 1488 +++++ .../public/pollution/624_contaminate_ref.bed | 128 + .../pollution/682_contaminate_cnvkit.bed | 1488 +++++ .../public/pollution/682_contaminate_ref.bed | 128 + script/public/pollution/contaminate_650.bed | 128 + script/run_pipeline.py | 18 +- script/run_wdl.py | 14 +- script/soft_bash | 13 + script/target_therapy_cnv.pl | 6 +- script/target_therapy_snpindel.pl | 4 +- wdl/alignment.wdl | 0 wdl/call_mutation.wdl | 0 wdl/chemo.wdl | 2 +- wdl/cnv.wdl | 0 wdl/fusion.wdl | 0 wdl/hereditary.wdl | 2 +- wdl/msi.wdl | 0 wdl/pollution.wdl | 65 + wdl/postprocess.wdl | 5 +- wdl/qc.wdl | 0 wdl/statistics.wdl | 0 wdl/tmb.wdl | 0 38 files changed, 9400 insertions(+), 120 deletions(-) create mode 100755 database/chemo_database.xlsx create mode 100755 database/hereditary_database.xlsx mode change 100644 => 100755 database/info.csv create mode 100755 script/filter_promoter.pl create mode 100755 script/pollution.py create mode 100644 script/public/pollution/160_contaminate_ref.bed create mode 100644 script/public/pollution/17_contaminate_ref.bed create mode 100644 script/public/pollution/624_contaminate_cnvkit.bed create mode 100644 script/public/pollution/624_contaminate_ref.bed create mode 100644 script/public/pollution/682_contaminate_cnvkit.bed create mode 100644 script/public/pollution/682_contaminate_ref.bed create mode 100644 script/public/pollution/contaminate_650.bed create mode 100755 script/soft_bash mode change 100644 => 100755 wdl/alignment.wdl mode change 100644 => 100755 wdl/call_mutation.wdl mode change 100644 => 100755 wdl/chemo.wdl mode change 100644 => 100755 wdl/cnv.wdl mode change 100644 => 100755 wdl/fusion.wdl mode change 100644 => 100755 wdl/hereditary.wdl mode change 100644 => 100755 wdl/msi.wdl create mode 100755 wdl/pollution.wdl mode change 100644 => 100755 wdl/postprocess.wdl mode change 100644 => 100755 wdl/qc.wdl mode change 100644 => 100755 wdl/statistics.wdl mode change 100644 => 100755 wdl/tmb.wdl diff --git a/database/chemo_database.xlsx b/database/chemo_database.xlsx new file mode 100755 index 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zwuX2gF1&14@-7#JXYZ&KKiPz@KQ$V?t3+G+c6Z2f9P>;rRBl^{r`L(1i*up}9(P0b zvxwd&XKkE-Zh2k1?D+G->w&}*dcHOu_edAsU@er+M3kKPu<@6tKWu0sEM$1`@Efmf zHvX1#xhI--CJ=E!g#!SvAS7wM1zCZCR$x6YaruZCRrqJj^i+G15N%0=sG(X)pqKMO(2fY>@Uz{k=yHJOc zcgb2P_&^#Jcbb9|@2Aq{gutN%Q#NvZ`;l1#p~WZv#bkjL4Zn3*85CW~DHQR5tb4_) z5#~WB3|qzzEg;uMKE_6wW#t4-R8C_4R#kdg+7z{O*EI?sk@x&oxK#y-ffymNuOd{M zz`I_`R){$7HaVuZy||2hPcr-*HXU244nw~MYKpMnvNR&eaMqmK61xk_2jn-u3!6S4 z%Zn8zM3#B3I$TvC9OF$vMu{qv@?}t{4>Kazwwac&wePu z{*tBtKT8y3P=D63zq0gqCHv{>cSB|V4Erx#`#WEy_*>%os}L}Ru%C(cv;4N>&G)Ol zcBTflKw}lKt(ldH-5)*vBPpp0(IN&>002WEL^6IG_?LyxjK3{_oh^WWg8nmEf6WkX z>R(W>DbN!5Um4$ARGV[1]"; my $project = $ARGV[2]; -my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/"; +# my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/"; +my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase"; -print "Cnv过滤使用public路径：$public_path\n"; +print "Cnv过滤使用database路径：$database_path\n"; my $cnv = info(); my @cnv_list = @$cnv; @@ -22,7 +23,7 @@ print OUT join("\t", (@head[0 .. 4], "ref_gene", "copy", @head[5 .. 9])), "\n"; while () { chomp; my @line = split(/\t/, $_); - my $cn = sprintf("%.2f", 2 ** (1 + $line[4])); + my $cn = sprintf("%.1f", 2 ** (1 + $line[4])); my @gene_list = split(/,/, $line[3]); my %uniq; foreach my $element (@gene_list) { @@ -38,7 +39,7 @@ while () { } sub info { - open INFO, "$public_path/info.csv"; + open INFO, "$database_path/info.csv"; # 读取并解析表头 my $header = ; chomp($header); diff --git a/script/filter_fusion.pl b/script/filter_fusion.pl index 84c9a04..07eac4b 100755 --- a/script/filter_fusion.pl +++ b/script/filter_fusion.pl @@ -6,8 +6,10 @@ die "usage:perl $0 depth_file input out project" unless @ARGV == 4; my ($depth_file, $input, $out, $project) = @ARGV; my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/"; +my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase"; print "Fusion过滤使用public路径：$public_path\n"; +print "Fusion过滤使用database路径：$database_path\n"; open IN, "$input"; open OUT1, "> $out"; @@ -189,7 +191,7 @@ sub gene2strand { } sub info { - open INFO, "$public_path/info.csv"; + open INFO, "$database_path/info.csv"; # 读取并解析表头 my $header = ; chomp($header); diff --git a/script/filter_longindel.pl b/script/filter_longindel.pl index 59a55a7..483daf0 100755 --- a/script/filter_longindel.pl +++ b/script/filter_longindel.pl @@ -4,9 +4,12 @@ use warnings; die "usage:perl $0 input out project" unless @ARGV == 3; my ($input, $out, $project) = @ARGV; -my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/"; +# my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/"; +# +# print "LongIndel过滤使用public路径：$public_path\n"; +my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase"; -print "LongIndel过滤使用public路径：$public_path\n"; +print "longindel过滤使用database路径：$database_path\n"; open IN, "$input"; open LONGINDEL, "> $out"; @@ -40,7 +43,7 @@ while () { } sub info { - open INFO, "$public_path/info.csv"; + open INFO, "$database_path/info.csv"; # 读取并解析表头 my $header = ; chomp($header); diff --git a/script/filter_promoter.pl b/script/filter_promoter.pl new file mode 100755 index 0000000..98868fd --- /dev/null +++ b/script/filter_promoter.pl @@ -0,0 +1,52 @@ +#!/usr/bin/env perl +use strict; + +my ($name, $output_dir, $project) = @ARGV; +die "useage:perl $0 codes_dir name output_dir project" unless @ARGV == 4; + +my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/"; +open INFO, "$public_path/info.csv"; +; +my @promoter; +while () { + chomp; + my @line = split(/\t/, $_); + if ($line[0] eq $project) { + if ($line[4] ne "NA") { + @promoter = split(/\//, $line[4]); + open PRMT, ">$output_dir/mutation/${name}.target.promoter.txt"; + } + } +} + +my @prmt; + +open IN2, "$output_dir/mutation/${name}.snp.indel.Somatic.annoall.hg19_multianno.txt"; +; +while () { + chomp; + my @line = split(/\t/, $_); + + if (@promoter and grep {$line[6] eq $_} @promoter) { + if ($line[5] =~ /UTR3|upstream/ and $line[17] < 0.01 + 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) { + my @var = split(/;/, $line[9]); + my $freq = (split(/:/, $line[-2]))[5]; + my $dp4 = join(",", (split(/:/, $line[-2]))[2, 4, -1]); + my $predict_benign = 0; + $predict_benign++ if ($line[50] eq "N" or $line[50] eq "P"); + $predict_benign++ if $line[56] eq "T"; + $predict_benign++ if $line[64] eq "T"; + if ($line[6] eq 'TERT') { + push @prmt, join("\t", @line[0 .. 9], $freq, $dp4, $predict_benign, @line[10, 11, 16, 18, $#line]) + if (($line[1] eq '1295228' and $line[4] eq 'A') or ($line[1] eq '1295250' and $line[4] eq 'A')); + } + } + } +} + +if (@prmt) { + print PRMT join("\t", @head[0 .. 9]), "\tFreq", "\tDP-AD-DP4", "\tpredict_benign(MutationTaster/FATHMM/MetaSVM)\t", join("\t", @head[10, 11, 16, 18]), "\tSTR", "\n"; + print PRMT join("\n", @prmt) . "\n"; +} + diff --git a/script/filter_snpindel.pl b/script/filter_snpindel.pl index 7be7d12..57efe45 100755 --- a/script/filter_snpindel.pl +++ b/script/filter_snpindel.pl @@ -243,7 +243,7 @@ sub blacklist { sub info { - open INFO, "$public_path/info.csv"; + open INFO, "$database_path/info.csv"; # 读取并解析表头 my $header = ; chomp($header); diff --git a/script/hereditary.py b/script/hereditary.py index 1fcaacd..c1b82ae 100755 --- a/script/hereditary.py +++ b/script/hereditary.py @@ -65,8 +65,7 @@ class HereditaryRun: if __name__ == "__main__": parser = argparse.ArgumentParser(description="hereditary Process Script") - parser.add_argument('-d', '--database', help="Path to hereditary_mut's database", - default='/home/zhangchao/project/pipeline/workflow/script/public/hereditary_database.xlsx') + parser.add_argument('-d', '--database', help="Path to hereditary_mut's database", required=True) parser.add_argument('-p', '--project', help="Project name", required=True) parser.add_argument('-n', '--name', help="Name for sample", required=True) parser.add_argument('-f', '--file', help="germline filter file", required=True) diff --git a/script/indication.pl b/script/indication.pl index 83c7ed4..8a344bd 100755 --- a/script/indication.pl +++ b/script/indication.pl @@ -2,14 +2,14 @@ use strict; use warnings; -my ($output_dir,$cancer_type)=@ARGV; -die "useage:perl $0 output_dir cancer_type" unless @ARGV==2; +my ($output_dir, $cancer_type) = @ARGV; +die "useage:perl $0 output_dir cancer_type" unless @ARGV == 2; my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase"; print "Indication药物注释使用路径：$database_path\n"; -open OUT,">$output_dir/mutation/indication.txt"; +open OUT, ">$output_dir/mutation/indication.txt"; print OUT "基因\t检测内容\t检测情况\t肿瘤类型\n"; ##本癌种FDA/NMPA/NCCN批准基因检测 =pod @@ -26,56 +26,58 @@ while(){ } =cut -open DIS,"/dataseq/jmdna/codes/reportbase/oncotree.cancertype.20230801.txt"; +open DIS, "$database_path/oncotree.cancertype.20230801.txt"; ; -my (%dis,@id,%dis2); -while(){ - chomp; - my @line=split(/\t/); - $dis{lc$line[2]}=$line[3]; - $dis{lc$line[4]}=$line[5]; - push @{$dis2{$line[0]}},lc$line[2]; - push @{$dis2{$line[0]}},lc$line[4]; - push @id,$line[0]; +my (%dis, @id, %dis2); +while () { + chomp; + my @line = split(/\t/); + $dis{lc $line[2]} = $line[3]; + # $dis{lc $line[4]} = $line[5]; + push @{$dis2{$line[0]}}, lc $line[2]; + # push @{$dis2{$line[0]}}, lc $line[4]; + push @id, $line[0]; } -foreach my $ID($cancer_type){ - my @family; - my @ids=split("",$ID); - for (my $i=1;$i<@ids;$i=$i+2){ - push @family,join("",@ids[0..$i]); - } - push @family,(grep{/^$ID/}@id); - foreach my $t(@family){ - push @{$dis2{$ID}},@{$dis2{$t}}; - } +foreach my $ID ($cancer_type) { + my @family; + my @ids = split("", $ID); + for (my $i = 1; $i < @ids; $i = $i + 2) { + push @family, join("", @ids[0 .. $i]); + } + push @family, (grep {/^$ID/} @id); + foreach my $t (@family) { + push @{$dis2{$ID}}, @{$dis2{$t}}; + } } -foreach my $key(keys(%dis2)){ - my %uniq; - @{$dis2{$key}}=grep{++$uniq{$_}<2}@{$dis2{$key}}; +foreach my $key (keys(%dis2)) { + my %uniq; + @{$dis2{$key}} = grep {++$uniq{$_} < 2} @{$dis2{$key}}; } ##靶向用药信息 -open THERAPY,"$database_path/targetTherapy.txt"; - ; +open THERAPY, "$database_path/targetTherapy.txt"; +; my %therapy; my %cancer; -while(){ - chomp; - my @line=split("\t"); - if($line[9] eq 'V' and $line[14] eq 'A' and (grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}) and $line[0]!~/,/){ - push @{$cancer{$line[0]}},$dis{lc$line[2]} if !(grep{$_ eq $dis{lc$line[2]}}@{$cancer{$line[0]}}); - if($line[1]=~/fusion/i){ - push @{$therapy{$line[0]}},'融合' if !(grep{$_ eq '融合'}@{$therapy{$line[0]}}); - }elsif($line[1] eq "Deletion" or $line[1]=~ /Amplification/){ - push @{$therapy{$line[0]}},'扩增' if !(grep{$_ eq '扩增'}@{$therapy{$line[0]}}); - }else{ - push @{$therapy{$line[0]}},'突变' if !(grep{$_ eq '突变'}@{$therapy{$line[0]}});; - } - } +while () { + chomp; + my @line = split("\t"); + if ($line[9] eq 'V' and $line[14] eq 'A' and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) and $line[0] !~ /,/) { + push @{$cancer{$line[0]}}, $dis{lc $line[2]} if !(grep {$_ eq $dis{lc $line[2]}} @{$cancer{$line[0]}}); + if ($line[1] =~ /fusion/i) { + push @{$therapy{$line[0]}}, '融合' if !(grep {$_ eq '融合'} @{$therapy{$line[0]}}); + } + elsif ($line[1] eq "Deletion" or $line[1] =~ /Amplification/) { + push @{$therapy{$line[0]}}, '扩增' if !(grep {$_ eq '扩增'} @{$therapy{$line[0]}}); + } + else { + push @{$therapy{$line[0]}}, '突变' if !(grep {$_ eq '突变'} @{$therapy{$line[0]}});; + } + } } -for my $gene(sort keys %therapy){ - print OUT "$gene\t",join("/",@{$therapy{$gene}}),"\t未检出变异\t",join("/",@{$cancer{$gene}}),"\n"; +for my $gene (sort keys %therapy) { + print OUT "$gene\t", join("/", @{$therapy{$gene}}), "\t未检出变异\t", join("/", @{$cancer{$gene}}), "\n"; } diff --git a/script/pollution.py b/script/pollution.py new file mode 100755 index 0000000..ef8776f --- /dev/null +++ b/script/pollution.py @@ -0,0 +1,287 @@ +#!/usr/bin/env python3 + +import argparse +import os + +import pandas as pd + + +def single_monitoring(name, vcf, bed, freq_range, output_dir): + 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) + + # bed 处理 + 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) + p_value_list.append(p_value) + select_vcf = os.path.join(output_dir, f'{name}_select.vcf') + with open(select_vcf, 'w') as output: + for header_line in vcf_header: + output.write(header_line) + for data_line in result_data: + output.write(data_line) + + count_normal = 0 + count_exception = 0 + for p_value in p_value_list: + if freq_range[0] <= p_value <= freq_range[1]: + count_normal += 1 + else: + count_exception += 1 + count_all = count_exception + count_normal + if count_all == 0: + z_score = 0 + else: + z_score = count_exception / count_all + + res = dict( + barcode=name, + count_normal=count_normal, + count_exception=count_exception, + z_score=z_score + ) + 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') + diff --git a/script/postprocess.py b/script/postprocess.py index c9af826..eafe461 100755 --- a/script/postprocess.py +++ b/script/postprocess.py @@ -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') diff --git a/script/public/pollution/160_contaminate_ref.bed b/script/public/pollution/160_contaminate_ref.bed new file mode 100644 index 0000000..cfdf615 --- /dev/null +++ b/script/public/pollution/160_contaminate_ref.bed @@ -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 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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 diff --git a/script/run_pipeline.py b/script/run_pipeline.py index 0cf5c42..b3ae3d8 100755 --- a/script/run_pipeline.py +++ b/script/run_pipeline.py @@ -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) diff --git a/script/run_wdl.py b/script/run_wdl.py index cebbc4b..3fdc868 100755 --- a/script/run_wdl.py +++ b/script/run_wdl.py @@ -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 $WORKFLOW/software/cromwell-51.jar run --inputs {jsfile_path} {wdl}' + # cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}' + cmd = f'{cmd3}; {cmd4}' # 记录开始时间 start_time = time.time() @@ -128,7 +129,8 @@ if __name__ == '__main__': parser.add_argument('-node', '--start_node', help="node begain to run; 'addQc', 'addAlignment', " "'addTarget', 'addFusion', 'addCnv', 'addMsi', 'addChemo'," - " 'addHcs, 'addTmb', addAutoReport' and also run more than one node ,like this 'addTarget,addFusion'", + " 'addHcs, 'addTmb', addAutoReport' and also run more than one node ," + "like this 'addTarget,addFusion'", default='addQc') args = parser.parse_args() diff --git a/script/soft_bash b/script/soft_bash new file mode 100755 index 0000000..36034e2 --- /dev/null +++ b/script/soft_bash @@ -0,0 +1,13 @@ +# 目录环境 +export WORKFLOW=/home/zhangchao/project/pipeline/workflow +export PUBLIC=$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 \ No newline at end of file diff --git a/script/target_therapy_cnv.pl b/script/target_therapy_cnv.pl index b436ed0..42af8d3 100755 --- a/script/target_therapy_cnv.pl +++ b/script/target_therapy_cnv.pl @@ -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 = ; chomp $h1; my %therapy; @@ -21,7 +21,7 @@ while () { ##药物翻译信息 -open DRUG, "/dataseq/jmdna/codes/reportbase/target_drug.txt"; +open DRUG, "$database_path/target_drug.txt"; my %drug; ; while () { @@ -55,7 +55,7 @@ sub drug { } -open DIS, "/dataseq/jmdna/codes/reportbase/oncotree.cancertype.20230801.txt"; +open DIS, "$database_path/oncotree.cancertype.20230801.txt"; ; my (%dis, @id, %dis2); while () { diff --git a/script/target_therapy_snpindel.pl b/script/target_therapy_snpindel.pl index b4f58d5..d0cef2c 100755 --- a/script/target_therapy_snpindel.pl +++ b/script/target_therapy_snpindel.pl @@ -114,7 +114,7 @@ while () { ($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 () { $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; diff --git a/wdl/alignment.wdl b/wdl/alignment.wdl old mode 100644 new mode 100755 diff --git a/wdl/call_mutation.wdl b/wdl/call_mutation.wdl old mode 100644 new mode 100755 diff --git a/wdl/chemo.wdl b/wdl/chemo.wdl old mode 100644 new mode 100755 index dc020a6..9abb28c --- a/wdl/chemo.wdl +++ b/wdl/chemo.wdl @@ -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 { diff --git a/wdl/cnv.wdl b/wdl/cnv.wdl old mode 100644 new mode 100755 diff --git a/wdl/fusion.wdl b/wdl/fusion.wdl old mode 100644 new mode 100755 diff --git a/wdl/hereditary.wdl b/wdl/hereditary.wdl old mode 100644 new mode 100755 index 02b2f2d..388877e --- a/wdl/hereditary.wdl +++ b/wdl/hereditary.wdl @@ -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 { diff --git a/wdl/msi.wdl b/wdl/msi.wdl old mode 100644 new mode 100755 diff --git a/wdl/pollution.wdl b/wdl/pollution.wdl new file mode 100755 index 0000000..854fb56 --- /dev/null +++ b/wdl/pollution.wdl @@ -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" + } +} \ No newline at end of file diff --git a/wdl/postprocess.wdl b/wdl/postprocess.wdl old mode 100644 new mode 100755 index 7211d7a..da1750b --- a/wdl/postprocess.wdl +++ b/wdl/postprocess.wdl @@ -31,8 +31,9 @@ workflow call_postprocess { String? mutation String? fusion String? cnv - String? msi + 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 } diff --git a/wdl/qc.wdl b/wdl/qc.wdl old mode 100644 new mode 100755 diff --git a/wdl/statistics.wdl b/wdl/statistics.wdl old mode 100644 new mode 100755 diff --git a/wdl/tmb.wdl b/wdl/tmb.wdl old mode 100644 new mode 100755