Mercurial > repos > ngsplot > ngsplot
comparison ngsplot_galaxytoolshed_v.10/ngsplot_main/runNGSplot.pl @ 12:f7debdafc7cb draft default tip
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author | ngsplot |
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date | Tue, 31 Mar 2015 10:15:27 -0400 |
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11:896dfca167fb | 12:f7debdafc7cb |
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1 #!/usr/bin/perl -w | |
2 use strict; | |
3 use File::Basename 'dirname'; | |
4 use File::Spec; | |
5 use Cwd 'abs_path'; | |
6 | |
7 my @inputs = @ARGV; | |
8 my @inputs2 = @inputs; | |
9 | |
10 my $genome_name = shift(@inputs); | |
11 my $genomic_region_source_type__genomic_region = shift(@inputs); | |
12 my $genomic_region_source_type__further_information = shift(@inputs); | |
13 my $genomic_region_source_type__interval_size = shift(@inputs); | |
14 my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_option = shift(@inputs); | |
15 my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size = shift(@inputs); | |
16 my $numsamples = shift(@inputs); | |
17 my $usepairs = shift(@inputs); | |
18 | |
19 #print STDERR "inputs @inputs\n"; | |
20 | |
21 my $randfile = rand(100)."\.config\.txt"; | |
22 my $randfile2 = $randfile; | |
23 $randfile2 =~ s/config\.txt/logfile/gm; | |
24 | |
25 my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile"); | |
26 open(FILE,">$outfile"); | |
27 | |
28 for (my $i=1;$i<=$numsamples;$i++) { | |
29 my $bamfile=shift(@inputs); | |
30 my $reffile=shift(@inputs); | |
31 my $usegenelist=shift(@inputs); | |
32 my $genelist=shift(@inputs); | |
33 my $title=shift(@inputs); | |
34 my $fraglen=shift(@inputs); | |
35 my $color=shift(@inputs); | |
36 if ($usepairs eq 'yes') { | |
37 syswrite(FILE, "$bamfile\:$reffile\t$genelist\t$title\t$fraglen\t$color\n"); | |
38 }else { | |
39 syswrite(FILE, "$bamfile\t$genelist\t$title\t$fraglen\t$color\n"); | |
40 } | |
41 } | |
42 close(FILE); | |
43 | |
44 my $gene_database = shift(@inputs); | |
45 my $randomly_sample = shift(@inputs); | |
46 my $gene_order = shift(@inputs); | |
47 my $knc = shift(@inputs); | |
48 my $mit = shift(@inputs); | |
49 my $nrs = shift(@inputs); | |
50 my $chunk_size = shift(@inputs); | |
51 my $quality_requirement = shift(@inputs); | |
52 my $standard_error = shift(@inputs); | |
53 my $radius_size = shift(@inputs); | |
54 my $flooding_fraction = shift(@inputs); | |
55 my $smooth_method = shift(@inputs); | |
56 my $shaded_area = shift(@inputs); | |
57 my $out_name = shift(@inputs); | |
58 my $out_avg_name = shift(@inputs); | |
59 my $out_hm_name = shift(@inputs); | |
60 | |
61 | |
62 my $G = $genome_name; | |
63 my $R = $genomic_region_source_type__genomic_region; | |
64 my $C = $outfile; | |
65 my $O = $out_name; | |
66 my $O2 = $out_avg_name; | |
67 my $O3 = $out_hm_name; | |
68 my $F = $genomic_region_source_type__further_information; | |
69 my $D = $gene_database; | |
70 my $L = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size; | |
71 my $N = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size; | |
72 my $RB = $radius_size; | |
73 my $S = $randomly_sample; | |
74 my $CS = $chunk_size; | |
75 my $MQ = $quality_requirement; | |
76 my $IN = $genomic_region_source_type__interval_size; | |
77 my $SE = $standard_error; | |
78 my $MW = $smooth_method; | |
79 my $H = $shaded_area; | |
80 my $GO = $gene_order; | |
81 my $KNC = $knc; | |
82 my $MIT = $mit; | |
83 my $NRS = $nrs; | |
84 my $FC = $flooding_fraction; | |
85 | |
86 if ($GO eq 'km') { | |
87 $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS"; | |
88 } | |
89 | |
90 my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2"); | |
91 open(FILE2,">>$logfile"); | |
92 my $cmd5="pwd >> $logfile 2>&1"; | |
93 system($cmd5); | |
94 | |
95 my $cmd=''; | |
96 if (($R eq 'tss')||($R eq 'tes')) { | |
97 $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; | |
98 }elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') { | |
99 if ($IN eq 'automatic') { | |
100 $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; | |
101 }else { | |
102 $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; | |
103 } | |
104 }elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') { | |
105 if ($IN eq 'automatic') { | |
106 $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; | |
107 }else { | |
108 $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; | |
109 } | |
110 } | |
111 my $cmd2="cp data.zip $O"; | |
112 my $cmd3="rm $outfile"; | |
113 my $cmd4="rm $logfile"; | |
114 syswrite(FILE2, "\n$cmd\n"); | |
115 syswrite(FILE2, "\n$cmd2\n"); | |
116 syswrite(FILE2, "\n$cmd3\n"); | |
117 syswrite(FILE2, "\n$cmd4\n\n"); | |
118 | |
119 system($cmd); | |
120 system($cmd2); | |
121 system($cmd3); | |
122 system($cmd4); | |
123 | |
124 close(FILE2); | |
125 | |
126 |