coverage_report: CoverageReport.pl annotate

annotate CoverageReport.pl @ 0:49788db492f7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7

author	iuc
date	Wed, 25 Oct 2017 12:37:17 -0400
parents
children

rev	line source
0 49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	1 #!/usr/bin/env perl
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	2 # load modules
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	3 use warnings;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	4 use Getopt::Std;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	5 use File::Basename;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	6 use Number::Format;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	7 use Cwd;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	8
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	9 my %opts;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	10
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	11 # number format
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	12 my $de = new Number::Format(-thousands_sep =>',',-decimal_point => '.');
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	13
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	14 ##########
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	15 ## opts ##
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	16 ##########
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	17 ## input files
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	18 # b : path to input (b)am file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	19 # t : path to input (t)arget regions in BED format
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	20 ## output files
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	21 # o : report pdf (o)utput file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	22 ## entries in the report
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	23 # r : Coverage per (r)egion (boolean)
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	24 # s : (s)ubregion coverage if average < specified (plots for positions along target region) (boolean)
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	25 # S : (S)ubregion coverage for ALL failed exons => use either s OR S or you will have double plots.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	26 # A : (A)ll exons will be plotted.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	27 # L : (L)ist failed exons instead of plotting
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	28 # m : (m)inimal Coverage threshold
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	29 # f : fraction of average as threshold
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	30 # n : sample (n)ame.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	31
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	32
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	33 getopts('b:t:o:rsSALm:n:f:', \%opts) ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	34
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	35 my $tmp = getcwd();
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	36 # make output directory in (tmp) working dir
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	37 our $wd = "$tmp/Coverage.".int(rand(1000));
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	38 while (-d $wd) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	39 $wd = "$tmp/Coverage.".int(rand(1000));
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	40 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	41 system("mkdir $wd");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	42
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	43 ## variables
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	44 our %commandsrun = ();
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	45 my ($thresh,$frac,$pdffile,$samplename,$totalmapped);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	46
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	47
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	48 if (!exists($opts{'b'}) \|\| !-e $opts{'b'}) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	49 die('Bam File not found');
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	50 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	51 if (!exists($opts{'t'}) \|\| !-e $opts{'t'}) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	52 die('Target File (BED) not found');
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	53 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	54
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	55 if (exists($opts{'m'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	56 $thresh = $opts{'m'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	57 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	58 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	59 $thresh = 40;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	60 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	61
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	62 if (exists($opts{'f'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	63 $frac = $opts{'f'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	64 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	65 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	66 $frac = 0.2;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	67 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	68
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	69 if (exists($opts{'o'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	70 $pdffile = $opts{'o'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	71 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	72 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	73 $pdffile = "$wd/CoverageReport.pdf";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	74 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	75
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	76
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	77 # 1. Global Summary => default
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	78 &GlobalSummary($opts{'b'}, $opts{'t'});
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	79
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	80 # 2. Coverage per position
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	81 &SubRegionCoverage($opts{'b'}, $opts{'t'});
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	82 our %filehash;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	83 if (exists($opts{'s'}) \|\| exists($opts{'S'}) \|\| exists($opts{'A'}) \|\| exists($opts{'L'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	84 system("mkdir $wd/SplitFiles");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	85 ## get position coverages
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	86 ## split input files
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	87 open IN, "$wd/Targets.Position.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	88 my $fileidx = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	89 my $currreg = '';
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	90 while (<IN>) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	91 my $line = $_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	92 chomp($line);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	93 my @p = split(/\t/,$line);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	94 my $reg = $p[0].'-'.$p[1].'-'.$p[2]; #.$p[3];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	95 my $ex = $p[3];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	96 if ($reg ne $currreg) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	97 ## new exon open new outfile
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	98 if ($currreg ne '') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	99 ## filehandle is open. close it
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	100 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	101 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	102 if (!exists($filehash{$reg})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	103 $fileidx++;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	104 $filehash{$reg}{'idx'} = $fileidx;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	105 $filehash{$reg}{'exon'} = $ex;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	106 open OUT, ">> $wd/SplitFiles/File_$fileidx.txt";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	107 $currreg = $reg;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	108 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	109 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	110 open OUT, ">> $wd/SplitFiles/File_".$filehash{$reg}{'idx'}.".txt";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	111 $currreg = $reg;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	112 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	113 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	114 ## print the line to the open filehandle.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	115 print OUT "$line\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	116 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	117 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	118 close IN;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	119
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	120 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	121
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	122 ## sort output files according to targets file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	123 if (exists($opts{'r'}) ) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	124 my %hash = ();
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	125 open IN, "$wd/Targets.Global.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	126 while (<IN>) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	127 chomp;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	128 my @p = split(/\t/,$_) ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	129 $hash{$p[3]} = $_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	130 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	131 close IN;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	132 open OUT, ">$wd/Targets.Global.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	133 open IN, $opts{'t'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	134 while (<IN>) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	135 chomp;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	136 my @p = split(/\t/,$_) ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	137 print OUT $hash{$p[3]} . "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	138 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	139 close IN;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	140 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	141 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	142
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	143
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	144 ####################################
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	145 ## PROCESS RESULTS & CREATE PLOTS ##
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	146 ####################################
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	147 system("mkdir $wd/Report");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	148
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	149 system("mkdir $wd/Rout");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	150 system("mkdir $wd/Plots");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	151
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	152 $samplename = $opts{'n'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	153 $samplename =~ s/_/\\_/g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	154 $samplename =~ s/\..+$//g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	155
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	156 # 0. Preamble
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	157 ## compose preamble
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	158 open OUT, ">$wd/Report/Report.tex";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	159 print OUT '\documentclass[a4paper,10pt]{article}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	160 print OUT '\usepackage[left=2cm,top=1.5cm,right=1.5cm,bottom=2.5cm,nohead]{geometry}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	161 print OUT '\usepackage{longtable}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	162 print OUT '\usepackage{fancyhdr}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	163 print OUT '\usepackage{fontspec}' . "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	164 print OUT '\usepackage{color}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	165 print OUT '\definecolor{grey}{RGB}{160,160,160}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	166 print OUT '\definecolor{darkgrey}{RGB}{100,100,100}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	167 print OUT '\definecolor{red}{RGB}{255,0,0}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	168 print OUT '\definecolor{orange}{RGB}{238,118,0}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	169 print OUT '\setlength\LTleft{0pt}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	170 print OUT '\setlength\LTright{0pt}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	171 print OUT '\begin{document}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	172 print OUT '\pagestyle{fancy}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	173 print OUT '\fancyhead{}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	174 print OUT '\renewcommand{\footrulewidth}{0.4pt}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	175 print OUT '\renewcommand{\headrulewidth}{0pt}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	176 print OUT '\fancyfoot[R]{\today\hspace{2cm}\thepage\ of \pageref{endofdoc}}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	177 print OUT '\fancyfoot[C]{}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	178 print OUT '\fancyfoot[L]{Coverage Report for ``'.$samplename.'"}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	179 print OUT '\let\oldsubsubsection=\subsubsection'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	180 print OUT '\renewcommand{\subsubsection}{%'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	181 print OUT ' \filbreak'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	182 print OUT ' \oldsubsubsection'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	183 print OUT '}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	184 # main title
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	185 print OUT '\section*{Coverage Report for ``'.$samplename.'"}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	186 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	187
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	188 # 1. Summary Report
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	189 # Get samtools flagstat summary of BAM file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	190 my $flagstat = `samtools flagstat $opts{'b'}`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	191 my @s = split(/\n/,$flagstat);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	192 # Get number of reads mapped in total
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	193 ## updated on 2012-10-1 !!
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	194 $totalmapped = $s[2];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	195 $totalmapped =~ s/^(\d+)(\s.+)/$1/;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	196
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	197 if ( not $totalmapped){
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	198 exit;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	199 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	200
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	201 # count columns
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	202 my $head = `head -n 1 $wd/Targets.Global.Coverage`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	203 chomp($head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	204 my @cols = split(/\t/,$head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	205 my $nrcols = scalar(@cols);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	206 my $covcol = $nrcols - 3;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	207 # get min/max/median/average coverage => values
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	208 my $covs = `cut -f $covcol $wd/Targets.Global.Coverage`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	209 my @coverages = split(/\n/,$covs);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	210 my ($eavg,$med,$min,$max,$first,$third,$ontarget) = arraystats(@coverages);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	211 my $spec = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	212 $spec=sprintf("%.1f",($ontarget / $totalmapped)*100);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	213 # get min/max/median/average coverage => boxplot in R
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	214 open OUT, ">$wd/Rout/boxplot.R";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	215 print OUT 'coverage <- read.table("../Targets.Global.Coverage",as.is=TRUE,sep="\t",header=FALSE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	216 print OUT 'coverage <- coverage[,'.$covcol.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	217 print OUT 'png(file="../Plots/CoverageBoxPlot.png", bg="white", width=240, height=480)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	218 print OUT 'boxplot(coverage,range=1.5,main="Target Region Coverage")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	219 print OUT 'graphics.off()'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	220 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	221 system("cd $wd/Rout && Rscript boxplot.R") == 0 \|\| die "Could not run boxplot.R with following error '$!'\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	222
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	223 ## global nt coverage plot
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	224 ## use perl to make histogram (lower memory)
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	225 open IN, "$wd/Targets.Position.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	226 my %dens;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	227 my $counter = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	228 my $sum = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	229 my $avg = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	230
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	231 while (<IN>) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	232 chomp();
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	233 my @p = split(/\t/);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	234 $sum += $p[-1];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	235 $counter++;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	236 if (defined($dens{$p[-1]})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	237 $dens{$p[-1]}++;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	238 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	239 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	240 $dens{$p[-1]} = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	241 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	242 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	243 $avg = $sum/$counter;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	244 close IN;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	245 open OUT, ">$wd/Rout/hist.txt";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	246 if (!defined($dens{'0'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	247 $dens{'0'} = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	248 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	249 foreach (keys(%dens)) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	250 print OUT "$_;$dens{$_}\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	251 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	252 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	253 open OUT, ">$wd/Rout/ntplot.R";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	254 # read coverage hist in R to plot
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	255 print OUT 'coverage <- read.table("hist.txt" , as.is = TRUE, header=FALSE,sep=";")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	256 print OUT 'mincov <- '."$thresh \n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	257 print OUT "avg <- round($avg,digits=8)\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	258 print OUT "colnames(coverage) <- c('cov','count')\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	259 print OUT 'coverage$cov <- coverage$cov / avg'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	260 print OUT 'rep <- which(coverage$cov > 1)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	261 print OUT 'coverage[coverage$cov > 1,1] <- 1'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	262 print OUT 'values <- coverage[coverage$cov < 1,]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	263 print OUT 'values <- rbind(values,c(1,sum(coverage[coverage$cov == 1,"count"])))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	264 print OUT 'values <- values[order(values$cov),]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	265 print OUT 'prevcount <- 0'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	266 # make cumulative count data frame
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	267 print OUT 'for (i in rev(values$cov)) {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	268 print OUT ' values[values$cov == i,"count"] <- prevcount + values[values$cov == i,"count"]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	269 print OUT ' prevcount <- values[values$cov == i,"count"]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	270 print OUT '}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	271 print OUT 'values$count <- values$count / (values[values$cov == 0,"count"] / 100)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	272 # get some values to plot lines.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	273 print OUT 'mincov.x <- mincov/avg'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	274 print OUT 'if (mincov/avg <= 1) {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	275 print OUT ' ii <- which(values$cov == mincov.x)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	276 print OUT ' if (length(ii) == 1) {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	277 print OUT ' mincov.y <- values[ii[1],"count"]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	278 print OUT ' } else {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	279 print OUT ' i1 <- max(which(values$cov < mincov.x))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	280 print OUT ' i2 <- min(which(values$cov > mincov.x))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	281 print OUT ' mincov.y <- ((values[i2,"count"] - values[i1,"count"])/(values[i2,"cov"] - values[i1,"cov"]))*(mincov.x - values[i1,"cov"]) + values[i1,"count"]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	282 print OUT ' }'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	283 print OUT '}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	284 # open output image and create plot
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	285 print OUT 'png(file="../Plots/CoverageNtPlot.png", bg="white", width=540, height=480)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	286 print OUT 'par(xaxs="i",yaxs="i")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	287 print OUT 'plot(values$cov,values$count,ylim=c(0,100),pch=".",main="Cumulative Normalised Base-Coverage Plot",xlab="Normalizalised Coverage",ylab="Cumulative Nr. Of Bases")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	288 print OUT 'lines(values$cov,values$count)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	289 print OUT 'if (mincov.x <= 1) {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	290 print OUT ' lines(c(mincov.x,mincov.x),c(0,mincov.y),lty=2,col="darkgreen")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	291 print OUT ' lines(c(0,mincov.x),c(mincov.y,mincov.y),lty=2,col="darkgreen")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	292 print OUT ' text(1,(95),pos=2,col="darkgreen",labels="Threshold: '.$thresh.'x")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	293 print OUT ' text(1,(91),pos=2,col="darkgreen",labels=paste("%Bases: ",round(mincov.y,2),"%",sep=""))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	294 print OUT '} else {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	295 print OUT ' text(1,(95),pos=2,col="darkgreen",labels="Threshold ('.$thresh.'x) > Average")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	296 print OUT ' text(1,(91),pos=2,col="darkgreen",labels="Plotting impossible")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	297 print OUT '}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	298 print OUT 'frac.x <- '."$frac\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	299 print OUT 'ii <- which(values$cov == frac.x)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	300 print OUT 'if (length(ii) == 1) {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	301 print OUT ' frac.y <- values[ii[1],"count"]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	302 print OUT '} else {'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	303 print OUT ' i1 <- max(which(values$cov < frac.x))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	304 print OUT ' i2 <- min(which(values$cov > frac.x))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	305 print OUT ' frac.y <- ((values[i2,"count"] - values[i1,"count"])/(values[i2,"cov"] - values[i1,"cov"]))*(frac.x - values[i1,"cov"]) + values[i1,"count"]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	306 print OUT '}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	307 print OUT 'lines(c(frac.x,frac.x),c(0,frac.y),lty=2,col="red")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	308 print OUT 'lines(c(0,frac.x),c(frac.y,frac.y),lty=2,col="red")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	309 #iprint OUT 'text((frac.x+0.05),(frac.y - 2),pos=4,col="red",labels=paste(frac.x," x Avg.Cov : ",round(frac.x * avg,2),"x",sep="" ))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	310 #print OUT 'text((frac.x+0.05),(frac.y-5),pos=4,col="red",labels=paste("%Bases: ",round(frac.y,2),"%",sep=""))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	311 print OUT 'text(1,86,pos=2,col="red",labels=paste(frac.x," x Avg.Cov : ",round(frac.x * avg,2),"x",sep="" ))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	312 print OUT 'text(1,82,pos=2,col="red",labels=paste("%Bases: ",round(frac.y,2),"%",sep=""))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	313
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	314 print OUT 'graphics.off()'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	315
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	316 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	317 system("cd $wd/Rout && Rscript ntplot.R") == 0 \|\| die "Could not run ntplot.R with following error '$!'\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	318 ## PRINT TO .TEX FILE
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	319 open OUT, ">>$wd/Report/Report.tex";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	320 # average coverage overviews
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	321 print OUT '\subsection*{Overall Summary}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	322 print OUT '{\small ';
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	323 # left : boxplot
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	324 print OUT '\begin{minipage}{0.3\linewidth}\centering'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	325 print OUT '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/CoverageBoxPlot.png}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	326 print OUT '\end{minipage}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	327 # right : cum.cov.plot
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	328 print OUT '\hspace{0.6cm}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	329 print OUT '\begin{minipage}{0.65\linewidth}\centering'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	330 print OUT '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/CoverageNtPlot.png}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	331 print OUT '\end{minipage} \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	332 ## next line
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	333 print OUT '\begin{minipage}{0.48\linewidth}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	334 print OUT '\vspace{-1.2em}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	335 print OUT '\begin{tabular}{ll}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	336 # bam statistics
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	337 print OUT '\multicolumn{2}{l}{\textbf{\underline{Samtools Flagstat Summary}}} \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	338 foreach (@s) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	339 $_ =~ m/^(\d+)\s(.+)$/;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	340 my $one = $1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	341 my $two = $2;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	342 $two =~ s/\s\+\s0\s//;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	343 $two = ucfirst($two);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	344 $one =~ s/%/\\%/g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	345 # remove '+ 0 ' from front
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	346 $two =~ s/\+\s0\s//;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	347 # remove trailing from end
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	348 $two =~ s/(\s\+.)\|(:.)/\)/;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	349 $two =~ s/%/\\%/g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	350 $two =~ s/>=/\$\\ge\$/g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	351 $two = ucfirst($two);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	352 print OUT '\textbf{'.$two.'} & '.$one.' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	353 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	354 print OUT '\end{tabular}\end{minipage}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	355 print OUT '\hspace{1.5cm}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	356 # target coverage statistics
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	357 print OUT '\begin{minipage}{0.4\linewidth}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	358 #print OUT '\vspace{-4.8em}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	359 print OUT '\begin{tabular}{ll}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	360 print OUT '\multicolumn{2}{l}{\textbf{\underline{Target Region Coverage}}} \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	361 print OUT '\textbf{Number of Target Regions} & '.scalar(@coverages).' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	362 print OUT '\textbf{Minimal Region Coverage} & '.$min.' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	363 print OUT '\textbf{25\% Region Coverage} & '.$first.' \\\\'. "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	364 print OUT '\textbf{50\% (Median) Region Coverage} & '.$med.' \\\\'. "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	365 print OUT '\textbf{75\% Region Coverage} & '.$third.' \\\\'. "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	366 print OUT '\textbf{Maximal Region Coverage} & '.$max.' \\\\'. "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	367 print OUT '\textbf{Average Region Coverage} & '.int($eavg).' \\\\'. "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	368 print OUT '\textbf{Mapped On Target} & '.$spec.' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	369 print OUT '\multicolumn{2}{l}{\textbf{\underline{Target Base Coverage }}} \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	370 print OUT '\textbf{Number of Target Bases} & '.$counter.' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	371 print OUT '\textbf{Average Base Coverage} & '.int($avg).' \\\\'. "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	372 print OUT '\textbf{Non-Covered Bases} & '.$dens{'0'}.' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	373 #print OUT '\textbf{Bases Covered $ge$ '.$frac.'xAvg.Cov} & '.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	374 print OUT '\end{tabular}\end{minipage}}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	375 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	376
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	377 # 2. GLOBAL COVERAGE OVERVIEW PER GENE
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	378 my @failedexons;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	379 my @allexons;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	380 my @allregions;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	381 my @failedregions;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	382 if (exists($opts{'r'}) \|\| exists($opts{'s'}) \|\| exists($opts{'S'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	383 # count columns
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	384 my $head = `head -n 1 $wd/Targets.Global.Coverage`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	385 chomp($head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	386 my @cols = split(/\t/,$head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	387 my $nrcols = scalar(@cols);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	388 my $covcol = $nrcols - 3;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	389 # Coverage Plots for each gene => barplots in R, table here.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	390 open IN, "$wd/Targets.Global.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	391 my $currgroup = '';
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	392 my $startline = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	393 my $stopline = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	394 my $linecounter = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	395 my $nrcol=0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	396 while (<IN>) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	397 $linecounter++;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	398 chomp($_);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	399 my @c = split(/\t/,$_);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	400 push(@allregions,$c[0].'-'.$c[1].'-'.$c[2]);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	401 my $group = $c[3];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	402 ## coverage failure?
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	403 if ($c[$nrcol-1] < 1 \|\| $c[$covcol-1] < $thresh) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	404 push(@failedexons,$group);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	405 push(@failedregions,$c[0].'-'.$c[1].'-'.$c[2]);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	406 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	407 ## store exon
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	408 push(@allexons,$group);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	409 ## extract and check gene
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	410 $group =~ s/^(\S+)[\\|\s](.+)/$1/;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	411
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	412 my $scale;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	413 if ($group ne $currgroup ) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	414 if ($currgroup ne '') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	415 # new gene, make plot.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	416 open OUT, ">$wd/Rout/barplot.R";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	417 print OUT 'coveragetable <- read.table("../Targets.Global.Coverage",as.is=TRUE,sep="\t",header=FALSE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	418 print OUT 'coverage <- coveragetable[c('.$startline.':'.$stopline.'),'.$covcol.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	419 print OUT 'entries <- coveragetable[c('.$startline.':'.$stopline.'),4]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	420 print OUT 'entries <- sub("\\\\S+\\\\\|","",entries,perl=TRUE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	421 print OUT 'coverage[coverage < 1] <- 1'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	422 print OUT 'colors <- c(rep("grey",length(coverage)))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	423 # coverage not whole target region => orange
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	424 print OUT 'covperc <- coveragetable[c('.$startline.':'.$stopline.'),'.$nrcols.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	425 print OUT 'colors[covperc<1] <- "orange"'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	426 # coverage below threshold => red
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	427 print OUT 'colors[coverage<'.$thresh.'] <- "red"'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	428
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	429 if ($stopline - $startline > 20) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	430 $scale = 2;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	431 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	432 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	433 $scale = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	434 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	435 my $width = 480 * $scale;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	436 my $height = 240 * $scale;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	437 print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	438 print OUT 'ylim = c(0,max(max(log10(coverage),log10('.($thresh+20).'))))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	439 print OUT 'mp <- barplot(log10(coverage),col=colors,main="Exon Coverage for '.$currgroup.'",ylab="Log10(Coverage)",ylim=ylim)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	440 print OUT 'text(mp, log10(coverage) + '.(0.4/$scale).',format(coverage),xpd = TRUE,srt=90)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	441 print OUT 'text(mp,par("usr")[3]-0.05,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	442 print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	443 print OUT 'graphics.off()'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	444 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	445 system("cd $wd/Rout && Rscript barplot.R") == 0 \|\| die "Could not run barplot.R with following error '$!'\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	446 if ($scale == 1) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	447 push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	448 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	449 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	450 push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	451 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	452
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	453 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	454 $currgroup = $group;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	455 $startline = $linecounter;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	456 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	457 $stopline = $linecounter;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	458 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	459 close IN;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	460 if ($currgroup ne '') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	461 # last gene, make plot.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	462 open OUT, ">$wd/Rout/barplot.R";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	463 print OUT 'coveragetable <- read.table("../Targets.Global.Coverage",as.is=TRUE,sep="\t",header=FALSE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	464 print OUT 'coverage <- coveragetable[c('.$startline.':'.$stopline.'),'.$covcol.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	465 print OUT 'entries <- coveragetable[c('.$startline.':'.$stopline.'),4]'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	466 print OUT 'entries <- sub("\\\\S+\\\\\|","",entries,perl=TRUE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	467 print OUT 'coverage[coverage < 1] <- 1'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	468 print OUT 'colors <- c(rep("grey",length(coverage)))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	469 print OUT 'colors[coverage<'.$thresh.'] <- "red"'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	470
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	471 if ($stopline - $startline > 20) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	472 $scale = 2;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	473 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	474 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	475 $scale = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	476 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	477 my $width = 480 * $scale;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	478 my $height = 240 * $scale;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	479 print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	480 print OUT 'ylim = c(0,max(max(log10(coverage),log10('.($thresh+20).'))))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	481 print OUT 'mp <- barplot(log10(coverage),col=colors,main="Exon Coverage for '.$currgroup.'",ylab="Log10(Coverage)", ylim=ylim)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	482 print OUT 'text(mp, log10(coverage) + log10(2),format(coverage),xpd = TRUE,srt=90)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	483 print OUT 'text(mp,par("usr")[3]-0.1,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	484 print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	485 print OUT 'graphics.off()'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	486 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	487 system("cd $wd/Rout && Rscript barplot.R") == 0 \|\| die "Could not run barplot.R with following error '$!'\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	488 if ($scale == 1) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	489 push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	490 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	491 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	492 push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	493 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	494 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	495 ## print to TEX
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	496 open OUT, ">>$wd/Report/Report.tex";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	497 print OUT '\subsection*{Gene Summaries}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	498 print OUT '\underline{Legend:} \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	499 print OUT '{\color{red}\textbf{RED:} Coverage did not reach set threshold of '.$thresh.'} \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	500 print OUT '{\color{orange}\textbf{ORANGE:} Coverage was incomplete for the exon. Overruled by red.} \\\\' ."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	501 my $col = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	502 foreach (@small) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	503 if ($col > 2) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	504 $col = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	505 print OUT "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	506 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	507 print OUT '\begin{minipage}{0.5\linewidth}\centering'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	508 print OUT $_."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	509 print OUT '\end{minipage}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	510 $col++;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	511 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	512 ## new line
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	513 if ($col == 2) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	514 print OUT '\\\\'." \n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	515 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	516 foreach(@large) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	517 print OUT $_."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	518 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	519 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	520
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	521 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	522
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	523 # 3. Detailed overview of failed exons (globally failed)
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	524 if (exists($opts{'s'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	525 # count columns
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	526 my $head = `head -n 1 $wd/Targets.Position.Coverage`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	527 chomp($head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	528 my $subtitle;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	529 my @cols = split(/\t/,$head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	530 my $nrcols = scalar(@cols);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	531 my $covcol = $nrcols;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	532 my $poscol = $nrcols -1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	533 # tex section header
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	534 open TEX, ">>$wd/Report/Report.tex";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	535 print TEX '\subsection*{Failed Exon Plots}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	536 $col = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	537 print TEX '\underline{NOTE:} Only exons with global coverage $<$'.$thresh.' or incomplete coverage were plotted \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	538 foreach(@failedregions) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	539 if ($col > 2) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	540 $col = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	541 print TEX "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	542 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	543 # which exon
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	544 my $region = $_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	545 my $exon = $filehash{$region}{'exon'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	546 # link exon to tmp file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	547 my $exonfile = "$wd/SplitFiles/File_".$filehash{$region}{'idx'}.".txt";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	548 ## determine transcript orientation and location
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	549 my $firstline = `head -n 1 $exonfile`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	550 my @firstcols = split(/\t/,$firstline);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	551 my $orient = $firstcols[5];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	552 my $genomicchr = $firstcols[0];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	553 my $genomicstart = $firstcols[1];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	554 my $genomicstop = $firstcols[2];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	555 if ($orient eq '+') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	556 $bps = $genomicstop - $genomicstart + 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	557 $subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."+".$de->format_number($genomicstop);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	558 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	559 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	560 $bps = $genomicstop - $genomicstart + 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	561 $subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."-".$de->format_number($genomicstop);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	562 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	563 # print Rscript
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	564 open OUT, ">$wd/Rout/exonplot.R";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	565 print OUT 'coveragetable <- read.table("'.$exonfile.'",as.is=TRUE,sep="\t",header=FALSE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	566 print OUT 'coverage <- coveragetable[,'.$covcol.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	567 print OUT 'coverage[coverage < 1] <- 1'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	568 print OUT 'positions <- coveragetable[,'.$poscol.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	569
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	570 my $width = 480 ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	571 my $height = 240 ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	572 my $exonstr = $exon;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	573 $exonstr =~ s/\s/_/g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	574 $exon =~ s/_/ /g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	575 $exon =~ s/\\|/ /g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	576 print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	577 print OUT 'ylim = c(0,log10(max(max(coverage),'.($thresh+10).')))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	578 if ($orient eq '-') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	579 print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",xlim=rev(range(positions)),sub="(Transcribed from minus strand)")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	580 print OUT 'mtext("'.$subtitle.'")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	581 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	582 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	583 print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",sub="(Transcribed from plus strand)")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	584 print OUT 'mtext("'.$subtitle.'")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	585 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	586 print OUT 'lines(positions,log10(coverage))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	587 print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	588 print OUT 'failedpos <- positions[coverage<'.$thresh.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	589 print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	590 print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	591 print OUT 'graphics.off()'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	592 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	593 # run R script
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	594 system("cd $wd/Rout && Rscript exonplot.R")== 0 \|\| die "Could not run exonplot.R with following error '$!'\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	595 # Add to .TEX
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	596 print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	597 print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	598 print TEX '\end{minipage}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	599 $col++;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	600 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	601 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	602
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	603 ## plot failed (subregion) or all exons
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	604 if (exists($opts{'S'}) \|\| exists($opts{'A'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	605 # count columns
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	606 my $head = `head -n 1 $wd/Targets.Position.Coverage`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	607 chomp($head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	608 my @cols = split(/\t/,$head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	609 my $nrcols = scalar(@cols);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	610 my $covcol = $nrcols;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	611 my $poscol = $nrcols -1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	612 # tex section header
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	613 open TEX, ">>$wd/Report/Report.tex";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	614 print TEX '\subsection*{Failed Exon Plots}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	615 if (exists($opts{'S'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	616 print TEX '\underline{NOTE:} ALL exons were tested for local coverage $<$'.$thresh.' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	617 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	618 elsif (exists($opts{'A'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	619 print TEX '\underline{NOTE:} ALL exons are plotted, regardless of coverage \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	620 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	621 $col = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	622 foreach(@allregions) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	623 if ($col > 2) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	624 $col = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	625 print TEX "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	626 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	627 # which exon
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	628 my $region = $_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	629 my $exon = $filehash{$region}{'exon'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	630 # grep exon to tmp file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	631 my $exonfile = "$wd/SplitFiles/File_".$filehash{$region}{'idx'}.".txt";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	632 ## determine transcript orientation.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	633 my $firstline = `head -n 1 $exonfile`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	634 my @firstcols = split(/\t/,$firstline);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	635 my $orient = $firstcols[5];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	636 my $genomicchr = $firstcols[0];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	637 my $genomicstart = $firstcols[1];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	638 my $genomicstop = $firstcols[2];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	639 my $subtitle;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	640
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	641 if ($orient eq '+') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	642 my $bps = $genomicstop - $genomicstart + 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	643 $subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."+".$de->format_number($genomicstop);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	644
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	645 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	646 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	647 my $bps = $genomicstop - $genomicstart + 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	648 $subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."-".$de->format_number($genomicstop);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	649
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	650 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	651
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	652 # check if failed
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	653 if (exists($opts{'S'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	654 my $cs = `cut -f $covcol '$exonfile' `;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	655 my @c = split(/\n/,$cs);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	656 @c = sort { $a <=> $b } @c;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	657 if ($c[0] >= $thresh) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	658 # lowest coverage > threshold => skip
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	659 next;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	660 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	661 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	662 # print Rscript
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	663 open OUT, ">$wd/Rout/exonplot.R";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	664 print OUT 'coveragetable <- read.table("'.$exonfile.'",as.is=TRUE,sep="\t",header=FALSE)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	665 print OUT 'coverage <- coveragetable[,'.$covcol.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	666 print OUT 'coverage[coverage < 1] <- 1'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	667 print OUT 'positions <- coveragetable[,'.$poscol.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	668 my $width = 480 ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	669 my $height = 240 ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	670 my $exonstr = $exon;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	671 $exonstr =~ s/\s/_/g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	672 $exon =~ s/_/ /g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	673 $exon =~ s/\\|/ /g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	674 print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	675 print OUT 'ylim = c(0,log10(max(max(coverage),'.($thresh+10).')))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	676 if ($orient eq '-') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	677 print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",xlim=rev(range(positions)),sub="(Transcribed from minus strand)")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	678 print OUT 'mtext("'.$subtitle.'")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	679 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	680 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	681 print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",sub="(Transcribed from plus strand)")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	682 print OUT 'mtext("'.$subtitle.'")'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	683 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	684
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	685 print OUT 'lines(positions,log10(coverage))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	686 print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	687 print OUT 'failedpos <- positions[coverage<'.$thresh.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	688 print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	689 print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	690 print OUT 'graphics.off()'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	691 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	692 # run R script
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	693 system("cd $wd/Rout && Rscript exonplot.R") == 0 \|\| die "Could not run exonplot.R with following error '$!'\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	694 # Add to .TEX
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	695 print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	696 print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	697 print TEX '\end{minipage}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	698 $col++;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	699 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	700 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	701 ## list failed exons
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	702 if (exists($opts{'L'})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	703 # count columns
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	704 my $subtitle;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	705 my $head = `head -n 1 $wd/Targets.Position.Coverage`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	706 chomp($head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	707 my @cols = split(/\t/,$head);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	708 my $nrcols = scalar(@cols);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	709 my $covcol = $nrcols;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	710 my $poscol = $nrcols -1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	711 ## hash to print
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	712 # tex section header
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	713 open TEX, ">>$wd/Report/Report.tex";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	714 print TEX '\subsection*{List of Failed Exons}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	715 print TEX '\underline{NOTE:} ALL exons were tested for local coverage $<$'.$thresh.' \\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	716 print TEX '{\footnotesize\begin{longtable}[l]{@{\extracolsep{\fill}}llll}'."\n".'\hline'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	717 print TEX '\textbf{Target Name} & \textbf{Genomic Position} & \textbf{Avg.Coverage} & \textbf{Min.Coverage} \\\\'."\n".'\hline'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	718 print TEX '\endhead'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	719 print TEX '\hline '."\n".'\multicolumn{4}{r}{{\textsl{\footnotesize Continued on next page}}} \\\\ '."\n".'\hline' ."\n". '\endfoot' . "\n". '\endlastfoot' . "\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	720
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	721 $col = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	722 open IN, "$wd/Targets.Global.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	723 while (<IN>) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	724 chomp($_);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	725 my @p = split(/\t/,$_);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	726 my $region = $p[0].'-'.$p[1].'-'.$p[2];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	727 my $exon = $filehash{$region}{'exon'};
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	728 # grep exon to tmp file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	729 my $exonfile = "$wd/SplitFiles/File_".$filehash{$region}{'idx'}.".txt";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	730 ## determine transcript orientation.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	731 my $firstline = `head -n 1 $exonfile`;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	732 my @firstcols = split(/\t/,$firstline);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	733 my $orient = $firstcols[5];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	734 my $genomicchr = $firstcols[0];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	735 my $genomicstart = $firstcols[1];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	736 my $genomicstop = $firstcols[2];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	737
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	738 if ($orient eq '+') {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	739 my $bps = $genomicstop - $genomicstart + 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	740 $subtitle = "$genomicchr:".$de->format_number($genomicstart)."+".$de->format_number($genomicstop);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	741
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	742 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	743 else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	744 my $bps = $genomicstop - $genomicstart + 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	745 $subtitle = "$genomicchr:".$de->format_number($genomicstart)."-".$de->format_number($genomicstop);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	746 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	747
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	748 # check if failed
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	749 my $cs = `cut -f $covcol '$exonfile' `;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	750 my @c = split(/\n/,$cs);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	751 my ($avg,$med,$min,$max,$first,$third,$ontarget) = arraystats(@c);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	752
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	753 if ($min >= $thresh) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	754 # lowest coverage > threshold => skip
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	755 next;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	756 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	757
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	758 # print to .tex table
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	759 if (length($exon) > 30) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	760 $exon = substr($exon,0,27) . '...';
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	761 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	762 $exon =~ s/_/ /g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	763 $exon =~ s/\\|/ /g;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	764
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	765 print TEX "$exon & $subtitle & ".int($avg)." & $min ".'\\\\'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	766 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	767 close IN;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	768 print TEX '\hline'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	769 print TEX '\end{longtable}}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	770 close TEX;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	771 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	772
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	773
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	774 ## Close document
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	775 open OUT, ">>$wd/Report/Report.tex";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	776 print OUT '\label{endofdoc}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	777 print OUT '\end{document}'."\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	778 close OUT;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	779 system("cd $wd/Report && tectonic Report.tex") == 0 \|\| die "Could not run tectonic with following error '$!'\n";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	780
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	781 ## mv report to output file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	782 system("cp -f $wd/Report/Report.pdf '$pdffile'");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	783 ##create tar.gz file
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	784 system("mkdir $wd/Results");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	785 system("cp -Rf $wd/Plots $wd/Results/");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	786 system("cp -Rf $wd/Report/ $wd/Results/");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	787 if (-e "$wd/Targets.Global.Coverage") {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	788 system("cp -Rf $wd/Targets.Global.Coverage $wd/Results/");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	789 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	790 if (-e "$wd/Targets.Position.Coverage") {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	791 system("cp -Rf $wd/Targets.Position.Coverage $wd/Results/");
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	792 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	793
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	794
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	795 exit;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	796
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	797 ###############
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	798 ## FUNCTIONS ##
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	799 ###############
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	800 sub arraystats{
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	801 my @array = @_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	802 my $count = scalar(@array);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	803 @array = sort { $a <=> $b } @array;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	804 # median
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	805 my $median = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	806 if ($count % 2) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	807 $median = $array[int($count/2)];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	808 } else {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	809 $median = ($array[$count/2] + $array[$count/2 - 1]) / 2;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	810 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	811 # average
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	812 my $sum = 0;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	813 foreach (@array) { $sum += $_; }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	814 my $average = $sum / $count;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	815 # quantiles (rounded)
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	816 my $quart = int($count/4) ;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	817 my $first = $array[$quart];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	818 my $third = $array[($quart*3)];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	819 my $min = $array[0];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	820 my $max = $array[($count-1)];
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	821 return ($average,$median,$min,$max,$first,$third,$sum);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	822 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	823
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	824 sub GlobalSummary {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	825 my ($bam,$targets) = @_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	826
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	827 my $command = "cd $wd && coverageBed -abam $bam -b $targets > $wd/Targets.Global.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	828 if (exists($commandsrun{$command})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	829 return;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	830 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	831 system($command);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	832 $commandsrun{$command} = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	833 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	834
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	835 sub CoveragePerRegion {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	836 my ($bam,$targets) = @_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	837 my $command = "cd $wd && coverageBed -abam $bam -b $targets > $wd/Targets.Global.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	838 if (exists($commandsrun{$command})) {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	839 return;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	840 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	841 system($command);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	842 $commandsrun{$command} = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	843 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	844
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	845 sub SubRegionCoverage {
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	846 my ($bam,$targets) = @_;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	847 my $command = "cd $wd && coverageBed -abam $bam -b $targets -d > $wd/Targets.Position.Coverage";
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	848 system($command);
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	849 $commandsrun{$command} = 1;
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	850 }
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7 iuc parents: diff changeset	851

Mercurial > repos > iuc > coverage_report

annotate CoverageReport.pl @ 0:49788db492f7 draft default tip