Mercurial > repos > geert-vandeweyer > coverage_report

comparison CoverageReport.pl @ 24:fd788f9db899 draft

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Added (default) option to collapse repetitive bed files
author geert-vandeweyer
date Thu, 12 Feb 2015 08:51:37 -0500
parents 95062840f80f
children 6cb012c8497a
comparison
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23:a718420c834e 24:fd788f9db899
26 # m : (m)inimal Coverage threshold 26 # m : (m)inimal Coverage threshold
27 # f : fraction of average as threshold 27 # f : fraction of average as threshold
28 # n : sample (n)ame. 28 # n : sample (n)ame.
29 29
30 30
31 getopts('b:t:o:z:rsSALm:n:f:', \%opts) ; 31 getopts('b:t:o:z:rsSALm:n:f:T', \%opts) ;
32 32
33 # make output directory in (tmp) working dir 33 # make output directory in (tmp) working dir
34 our $wd = "/tmp/Coverage.".int(rand(1000)); 34 our $wd = "/tmp/Coverage.".int(rand(1000));
35 while (-d $wd) { 35 while (-d $wd) {
36 $wd = "/tmp/Coverage.".int(rand(1000)); 36 $wd = "/tmp/Coverage.".int(rand(1000));
37
37 } 38 }
38 system("mkdir $wd"); 39 system("mkdir $wd");
39 40
40 ## variables 41 ## variables
41 our %commandsrun = (); 42 our %commandsrun = ();
71 if (exists($opts{'z'})) { 72 if (exists($opts{'z'})) {
72 $tarfile = $opts{'z'}; 73 $tarfile = $opts{'z'};
73 } 74 }
74 else { 75 else {
75 $tarfile = "$wd/Results.tar.gz"; 76 $tarfile = "$wd/Results.tar.gz";
77 }
78
79 ## 0. Collapse overlapping target regions.
80 if (defined($opts{'T'})) {
81 my $targets = $opts{'t'};
82 my $tmptargets = "$wd/collapsedtargets.bed";
83 system("sort -k1,1 -k2,2n $targets > $wd/sorted.targets.bed");
84 system("bedtools merge -s -scores max -nms -i $wd/sorted.targets.bed > $tmptargets");
85 $opts{'t'} = $tmptargets;
76 } 86 }
77 87
78 # 1. Global Summary => default 88 # 1. Global Summary => default
79 &GlobalSummary($opts{'b'}, $opts{'t'}); 89 &GlobalSummary($opts{'b'}, $opts{'t'});
80 90