<commit_before>#!/usr/bin/perl -w

#use Getopt::Std;
use Getopt::Long qw(:config no_ignore_case);
use strict;

our ($opt_n, $opt_f, $opt_F, $opt_H, $opt_D, $opt_V, $opt_M, $opt_R);

my $ruledir = "/users/kdld047/work/NGS/Wee1";
my $filter_common_snp = "/group/cancer_informatics/tools_resources/NGS/genomes/hg19/Annotation/filter_common_snp.txt";
my $snpeffect_export_polymorphic = "/group/cancer_informatics/tools_resources/NGS/genomes/hg19/Annotation/snpeffect_export_Polymorphic.txt";
my $filter_common_artifacts = "/group/cancer_informatics/tools_resources/NGS/genomes/hg19/Annotation/filter_common_artifacts.txt";
my $actionable_hotspot = "/group/cancer_informatics/tools_resources/NGS/genomes/hg19/Annotation/actionable_hotspot.txt";
my $actionable = "/group/cancer_informatics/tools_resources/NGS/genomes/hg19/Annotation/actionable.txt";
my $compendia_ms7_hotspot = "/group/cancer_informatics/tools_resources/NGS/genomes/hg19/Annotation/Compendia.MS7.Hotspot.txt";

GetOptions ("n=s" => \$opt_n,
            "f=f" => \$opt_f,
            "F=f" => \$opt_F,
            "H|?" => \$opt_H,
            "D=i" => \$opt_D,
            "V=i" => \$opt_V,
            "M"   => \$opt_M,
            "R=f" => \$opt_R,
            "ruledir=s" => \$ruledir,
            "filter_common_snp=s" => \$filter_common_snp,
            "snpeffect_export_polymorphic=s" => \$snpeffect_export_polymorphic,
            "filter_common_artifacts=s" => \$filter_common_artifacts,
            "actionable_hotspot=s" => \$actionable_hotspot,
            "actionable=s" => \$actionable,
            "compendia_ms7_hotspot=s" => \$compendia_ms7_hotspot) or USAGE();

#getopts( 'HMn:f:F:D:V:R:' ) || USAGE();
$opt_H && USAGE();

my $tp53group1 = parseMut_tp53( "$ruledir/Rules/DNE.txt" );
my $tp53group2 = parseMut_tp53( "$ruledir/Rules/TA0-25.txt" );
my $tp53group3 = parseMut_tp53( "$ruledir/Rules/TA25-50_SOM_10x.txt" );
my %tp53critical_aa_pos;
my @tp53hg19splice = qw(7574034 7574035 7576851 7576852 7576927 7576928 7577017 7577018 7577156 7577157 7577497 7577498 7577609 7577610 7578175 7578176 7578290 7578291 7578369 7578370 7578555 7578556 7579310 7579311 7579591 7579592 7579698 7579699 7579722 7579723 7579837 7579838 7574033 7576926 7577155 7577608 7578289 7578554 7579590 7579721 7576853 7577019 7577499 7578177 7578371 7579312 7579700 7579839);
my %tp53hg19splice = map { ($_, 1); } @tp53hg19splice;<commit_msg>vardict2mut.pl: symlinks for annotation files for full compability with AP<commit_after>#!/usr/bin/perl -w

#use Getopt::Std;
use Getopt::Long qw(:config no_ignore_case);
use strict;

our ($opt_n, $opt_f, $opt_F, $opt_H, $opt_D, $opt_V, $opt_M, $opt_R);

my $ruledir = "/ngs/reference_data/genomes/Hsapiens/hg19/variation/rules";  # "/users/kdld047/work/NGS/Wee1";
my $annotation_dir = '/ngs/reference_data/genomes/Hsapiens/hg19/variation/cancer_informatics';  # "/ngs/reference_data/genomes/Hsapiens/hg19/variation/cancer_informatics";
my $filter_common_snp = "$annotation_dir/filter_common_snp.txt";
my $snpeffect_export_polymorphic = "$annotation_dir/snpeffect_export_Polymorphic.txt";
my $filter_common_artifacts = "$annotation_dir/filter_common_artifacts.txt";
my $actionable_hotspot = "$annotation_dir/actionable_hotspot.txt";
my $actionable = "$annotation_dir/actionable.txt";
my $compendia_ms7_hotspot = "$annotation_dir/Compendia.MS7.Hotspot.txt";

GetOptions ("n=s" => \$opt_n,
            "f=f" => \$opt_f,
            "F=f" => \$opt_F,
            "H|?" => \$opt_H,
            "D=i" => \$opt_D,
            "V=i" => \$opt_V,
            "M"   => \$opt_M,
            "R=f" => \$opt_R,
            "ruledir=s" => \$ruledir,
            "filter_common_snp=s" => \$filter_common_snp,
            "snpeffect_export_polymorphic=s" => \$snpeffect_export_polymorphic,
            "filter_common_artifacts=s" => \$filter_common_artifacts,
            "actionable_hotspot=s" => \$actionable_hotspot,
            "actionable=s" => \$actionable,
            "compendia_ms7_hotspot=s" => \$compendia_ms7_hotspot) or USAGE();

#getopts( 'HMn:f:F:D:V:R:' ) || USAGE();
$opt_H && USAGE();

my $tp53group1 = parseMut_tp53( "$ruledir/Rules/DNE.txt" );
my $tp53group2 = parseMut_tp53( "$ruledir/Rules/TA0-25.txt" );
my $tp53group3 = parseMut_tp53( "$ruledir/Rules/TA25-50_SOM_10x.txt" );
my %tp53critical_aa_pos;
my @tp53hg19splice = qw(7574034 7574035 7576851 7576852 7576927 7576928 7577017 7577018 7577156 7577157 7577497 7577498 7577609 7577610 7578175 7578176 7578290 7578291 7578369 7578370 7578555 7578556 7579310 7579311 7579591 7579592 7579698 7579699 7579722 7579723 7579837 7579838 7574033 7576926 7577155 7577608 7578289 7578554 7579590 7579721 7576853 7577019 7577499 7578177 7578371 7579312 7579700 7579839);
my %tp53hg19splice = map { ($_, 1); } @tp53hg19splice;
{'fraction_non_alphanumeric': 0.13959337665059737, 'fraction_numerical': 0.1645357367428212, 'mean_word_length': 4.314031180400891, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 33, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5781864', 'n_tokens_mistral': 2494, 'n_tokens_neox': 1887, 'n_words': 307}