Mercurial > repos > bioitcore > splicetrap

comparison bin/SpliceTrap_measure.pl @ 1:adc0f7765d85 draft

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planemo upload
author bioitcore
date Thu, 07 Sep 2017 15:06:58 -0400
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0:d4ca551ca300 1:adc0f7765d85
1 # Author: wuj@cshl.edu
2 use strict;
3 use Getopt::Long;
4 ####################
5 my %config=do "$ENV{HOME}/.SpliceTrap.pl.ini";
6 my $SrcFolder=$config{SrcFolder};
7 #my $SrcFolder="/data/zhang/wuj/tools/SpliceTrap.0.8";
8 ####################
9 my $MapSoftware="eland";
10 my $ReadFileFormat="";
11 my $ReadFile1Name="";
12 my $ReadFile2Name="";
13 my $CutoffLevel="H";
14 my $OutputPrefix="Result";
15 my $CutoffOnly=0;
16 my $ReadSize=36;
17
18 GetOptions (
19 "m:s"=>\$MapSoftware,
20 "f:s"=>\$ReadFileFormat,
21 "1:s"=>\$ReadFile1Name,
22 "2:s"=>\$ReadFile2Name,
23 "c:s"=>\$CutoffLevel,
24 "o:s"=>\$OutputPrefix,
25 "s:i"=>\$ReadSize,
26 # "local:s"=>\$local,
27 "rerun"=>\$CutoffOnly
28 );
29
30
31 my $InputParaDes=" Usage of the script (v0.82):
32 -m Mapping software: eland/bowtie/rmap
33 -f Read File Format: fasta/fastq
34 -1 Read File 1
35 -2 Read File 2
36 -c Cutoff Level:H/M/L
37 Means High, Middle or Low
38 -o Output prefix
39 -s Read Size 36
40 --rerun Only run the last step, which is filtering
41 ";
42
43 if($ReadFile1Name eq "" or $ReadFile2Name eq "" or $ReadFileFormat eq "")
44 {
45 print $InputParaDes;
46 exit;
47 }
48
49 if($ReadFileFormat ne "fastq" and $ReadFileFormat ne "fasta")
50 {
51 print $InputParaDes;
52 exit;
53
54 }
55
56 if($CutoffLevel ne "H" and $CutoffLevel ne "M" and $CutoffLevel ne "L")
57 {
58 print $InputParaDes;
59 exit;
60 }
61
62 my $dirname1=`dirname $ReadFile1Name`;
63 my $dirname2=`dirname $ReadFile2Name`;
64 if($dirname1 ne ".")
65 {
66 system("ln -s $ReadFile1Name ./");
67 }
68 if($dirname2 ne ".")
69 {
70 system("ln -s $ReadFile2Name ./");
71 }
72
73 $ReadFile1Name = `basename $ReadFile1Name`;
74 chomp($ReadFile1Name);
75 $ReadFile2Name = `basename $ReadFile2Name`;
76 chomp($ReadFile2Name);
77 my $start = time;
78 if($MapSoftware eq "bowtie")
79 {
80 print "=================STAGE 1 MAPPING===================\n";
81 system("bash $SrcFolder/mapping_bowtie.sh $ReadFile1Name $ReadFileFormat") if not $CutoffOnly;
82 system("bash $SrcFolder/mapping_bowtie.sh $ReadFile2Name $ReadFileFormat") if not $CutoffOnly;
83 print "STAGE 1 FINISHED IN ",time-$start," seconds\n";
84 print "=================STAGE 2 ESTIMATION================\n";
85
86 system("bash $SrcFolder/batch_para_cov10p_fit.sh $ReadFile1Name $ReadFile2Name $OutputPrefix $ReadSize") if not $CutoffOnly;
87 print "STAGE 2 FINISHED IN ",time-$start," seconds\n";
88 print "=================STAGE 3 CUTOFF====================\n";
89 system("bash $SrcFolder/apply_cutoff.sh $OutputPrefix $CutoffLevel");
90 print "STAGE 3 FINISHED IN ",time-$start," seconds\n";
91
92
93
94 }
95
96 if($MapSoftware eq "rmap")
97 {
98 print "=================STAGE 1 MAPPING===================\n";
99
100 system("bash $SrcFolder/mapping_rmap.sh $ReadFile1Name $ReadFileFormat") if not $CutoffOnly;
101 system("bash $SrcFolder/mapping_rmap.sh $ReadFile2Name $ReadFileFormat") if not $CutoffOnly;
102 print "=================STAGE 2 ESTIMATION================\n";
103
104 system("bash $SrcFolder/batch_para_cov10p_fit.sh $ReadFile1Name $ReadFile2Name $OutputPrefix $ReadSize") if not $CutoffOnly;
105 print "=================STAGE 3 CUTOFF====================\n";
106 system("bash $SrcFolder/apply_cutoff.sh $OutputPrefix $CutoffLevel");
107
108
109 }
110
111 print "============ALL DONE, OUTPUTFILE:$OutputPrefix.txt\n";