perl/bsvf/bsdbg

   1 #!/usr/bin/env perl
   2 use strict;
   3 use warnings;
   4 use Data::Dump qw(ddx);
   5
   6 use FindBin qw($RealBin);
   7 if ($FindBin::VERSION < 1.51) {
   8         warn "[!]Your Perl is too old, thus there can only be ONE `bsuit` file in your PATH. [FindBin Version: $FindBin::VERSION < 1.51]\n\n"
   9 }
  10 FindBin::again();
  11 use lib "$RealBin/lib";
  12 require BSuitLib;
  13 use Galaxy::IO::INI;
  14
  15 my %Cmd2Fun = (
  16         'prepare' => \&do_pre,
  17         'grep' => \&do_grep,
  18         'analyse' => \&do_analyse,
  19 );
  20
  21 sub ShowHelp() {
  22         die '[!]Available Commands are: [',join('],[',sort keys %Cmd2Fun),"], case insensitive.\n";
  23 }
  24 my $ShowHelp=0;
  25 if (@ARGV < 2) {
  26         warn "Usage: $0 <command> Human=hg19.fa,Virus=hbv.fa,bam=Sorted.bam,out=./test/\n";
  27         ShowHelp();
  28 }
  29 my $cmd=lc shift;
  30 my $cfgdat=shift;
  31 #die "[!]Config File [$cfgfile] NOT found !\n" unless -f $cfgfile;
  32 my %CFG = (
  33         human => '',
  34         virus => '',
  35         bam => '',
  36         out => './test'
  37 );
  38 for ( split /\,/,$cfgdat ) {
  39         my ($id,$val) = split /=/,$_;
  40         $id = lc $id;
  41         next unless exists $CFG{$id};
  42         $CFG{$id} = $val;
  43 }
  44 die "[!]Bam File [$CFG{'bam'}] NOT found !\n" unless -f $CFG{'bam'};
  45 my $cfgfile = $CFG{'out'} . '/prj.ini';
  46 my $thedir = $CFG{'out'} . '/Project1_aln';
  47 unless (-d $thedir) {
  48         File::Path::make_path($thedir,{verbose => 0,mode => 0755});
  49 }
  50 link $CFG{'bam'},$thedir.'/Test.bam';
  51
  52 open O,'>',$cfgfile;
  53 print O "
  54 [RefFiles]
  55 HostRef=$CFG{'human'}
  56 VirusRef=$CFG{'virus'}
  57
  58 [DataFiles]
  59 Test.1=xx_1.fq
  60 Test.2=xx_2.fq
  61
  62 [InsertSizes]
  63 Test=500
  64 Test.SD=50
  65
  66 [Output]
  67 WorkDir=$CFG{'out'}
  68 ProjectID=Project1
  69 ";
  70 close O;
  71
  72 our $DISABLE_REF_INDEX=1;
  73
  74 unless (exists $Cmd2Fun{$cmd}) {
  75         warn "[x]Unknown Command: [$cmd] !\n";
  76         ShowHelp();
  77 }
  78
  79 #our $CFGminMAPQ = 30;
  80 our $minHostDepth = 30;
  81 our $minSoftClip = 10;
  82 our $methly3BaseErrRate = 0.08;
  83 our $DEVELOP = 0;
  84 our $DEBUG = 1;
  85
  86 our $idbacmd = '--max_gap 100 --min_region 31 --min_contig 31 --mink 17 --maxk 89 --step 20';
  87 our $PathPrefix = "PATH=\"$RealBin/bin:\$PATH\";";
  88
  89 our $Config = Galaxy::IO::INI->new();
  90 $Config->read($cfgfile);
  91 #ddx \$Config;
  92
  93 warn "[!]Runing $0 [$cmd].\n";
  94
  95
  96
  97 our $RootPath = $Config->{'Output'}->{'WorkDir'};
  98 $RootPath =~ s/[\/\\]+$//g;
  99 our $ProjectID = $Config->{'Output'}->{'ProjectID'};
 100 warn "[!] Working on: [$ProjectID] @ [$RootPath]\n";
 101
 102 our $HostRefName = basename($Config->{'RefFiles'}->{'HostRef'});
 103 our $VirusRefName = basename($Config->{'RefFiles'}->{'VirusRef'});
 104 our $RefFilesSHA = getFilesHash($HostRefName,$VirusRefName);
 105
 106 our $RefConfig = Galaxy::IO::INI->new();
 107 our (%RefChrIDs,%VirusChrIDs);
 108
 109 $Cmd2Fun{'prepare'}($cfgfile);
 110
 111 if ($cmd ne 'prepare') {
 112         if ( -f "$RootPath/Ref/Ref.ini" ) {
 113                 $RefConfig->read("$RootPath/Ref/Ref.ini");
 114         } else {die "[x] Prepare INI not found ! [$RootPath/Ref/Ref.ini]\n";}
 115         my @RefChrID = split(',',$RefConfig->{$RefFilesSHA}->{'RefChrIDs'});
 116         my @VirusChrID = split(',',$RefConfig->{$RefFilesSHA}->{'VirusChrIDs'});
 117         for (@RefChrID) {
 118                 $RefChrIDs{$_} = $RefConfig->{$RefFilesSHA}->{$_};
 119         }
 120         $VirusChrIDs{$_} = $RefConfig->{$RefFilesSHA}->{$_} for @VirusChrID;
 121 }
 122
 123 $Cmd2Fun{$cmd}($cfgfile);       # If use `do $Cmd2Fun{$cmd}();`, the sub MUST return 1;
 124 warn "[!]done !\n";
 125
 126 # overlap = (min(end_mate1,end_mate2) - max(start_mate1,start_mate2)) http://sourceforge.net/p/bio-bwa/mailman/message/27028596/
 127
 128 # rsync -Lav --existing . ~/git/BS-viral-inte/