Mercurial > repos > big-tiandm > sirna_plant
comparison SampleDEGseqMerge.pl @ 21:9dcffd531c76 draft
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author | big-tiandm |
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date | Wed, 05 Nov 2014 21:09:35 -0500 |
parents | 07745c0958dd |
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20:2ed1e1728299 | 21:9dcffd531c76 |
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1 #!/usr/bin/perl -w | |
2 #Filename: | |
3 #Author: Tian Dongmei | |
4 #Email: chentt@big.ac.cn | |
5 #Date: 2014-05-21 | |
6 #Modified: | |
7 #Description: merged deg file and total information | |
8 my $version=1.00; | |
9 | |
10 use strict; | |
11 use Getopt::Long; | |
12 | |
13 my %opts; | |
14 GetOptions(\%opts,"i:s@","mark:s@","f:s","o=s","n=s","h"); | |
15 if (!(defined $opts{o} ) || defined $opts{h}) { #necessary arguments | |
16 &usage; | |
17 } | |
18 | |
19 my @filein=@{$opts{'i'}}; | |
20 my @mark=@{$opts{'mark'}}; | |
21 my $fileout=$opts{'o'}; | |
22 my $number=$opts{'n'}; | |
23 | |
24 my %hash; | |
25 open IN,"<$filein[0]"; #input file | |
26 | |
27 while (my $aline=<IN>) { | |
28 chomp $aline; | |
29 next if($aline=~/^\"/); | |
30 my @temp=split/\t/,$aline; | |
31 $hash{$temp[0]}=$temp[4]."\t".$temp[6]."\t".$temp[7]."\t".$temp[-1]; | |
32 } | |
33 close IN; | |
34 | |
35 for (my $i=1;$i<=$#filein;$i++) { | |
36 open IN,"<$filein[$i]"; #input file | |
37 | |
38 while (my $aline=<IN>) { | |
39 chomp $aline; | |
40 next if($aline=~/^\"/); | |
41 my @temp=split/\t/,$aline; | |
42 if (!(defined $hash{$temp[0]})) { | |
43 print "Not find $temp[0]in sample one!\n"; | |
44 next; | |
45 } | |
46 $hash{$temp[0]} .="\t".$temp[4]."\t".$temp[6]."\t".$temp[7]."\t".$temp[-1]; | |
47 } | |
48 close IN; | |
49 } | |
50 | |
51 open OUT,">$fileout"; #output file | |
52 my $deg_title; | |
53 foreach (@mark) { | |
54 $deg_title.="log2(Fold_change)\tp_value\tq_value\t".$_."\t"; | |
55 } | |
56 $deg_title=~s/\s+$//; | |
57 my %function; | |
58 my $title; | |
59 open F,"<$opts{f}"; | |
60 while (my $aline=<F>) { | |
61 chomp $aline; | |
62 if($aline=~/^\#/){ | |
63 my $title=$aline; | |
64 my @title=split/\t/,$aline; | |
65 $title[2+$number].="\t".$deg_title; | |
66 $title=join"\t",@title; | |
67 print OUT "$title\n"; | |
68 next; | |
69 } | |
70 my @temp=split/\t/,$aline; | |
71 $temp[2+$number].="\t".$hash{$temp[0]}; | |
72 my $temp=join"\t",@temp; | |
73 print OUT "$temp\n"; | |
74 | |
75 } | |
76 close F; | |
77 close OUT; | |
78 | |
79 sub usage{ | |
80 print <<"USAGE"; | |
81 Version $version | |
82 Usage: | |
83 $0 -i -o -mark -f | |
84 options: | |
85 -i input file # -i output_score.txt -i output_score.txt -i output_score.txt | |
86 -mark sample name # -mark sam1_VS_sam2 -mark sam1_VS_sam3 -mark sam2_VS_sam3 | |
87 -f cluster file | |
88 -n sample number | |
89 -o output file | |
90 -h help | |
91 USAGE | |
92 exit(1); | |
93 } | |
94 |