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comparison rapsodyn/filtersam_mapped_and_unique.pl @ 10:0a6c1cfe4dc8 draft

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Uploaded
author mcharles
date Mon, 19 Jan 2015 04:33:21 -0500
parents 3f7b0788a1c4
children
comparison
equal deleted inserted replaced
9:0e7c6fe60646 10:0a6c1cfe4dc8
1 #!/usr/bin/perl 1 #!/usr/bin/perl
2 #V1.1.0 manage empty files
2 #V1.0.1 added log, option parameters 3 #V1.0.1 added log, option parameters
3 use strict; 4 use strict;
4 use warnings; 5 use warnings;
5 use Getopt::Long; 6 use Getopt::Long;
6 7
7 my $input_sam_file; 8 my $input_sam_file;
8 my $output_sam_file; 9 my $output_sam_file;
9 my $log_file; 10 my $log_file;
11 my $empty_file=1;
10 12
11 my %bitscore_all; 13 my %bitscore_all;
12 my %bitscore_selected; 14 my %bitscore_selected;
13 15
14 GetOptions ( 16 GetOptions (
35 } 37 }
36 if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){ 38 if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){
37 my @fields_selected = split (/\s+/,$line); 39 my @fields_selected = split (/\s+/,$line);
38 if (($fields_selected[1]==83)||($fields_selected[1]==163)||($fields_selected[1]==147)||($fields_selected[1]==99)){ 40 if (($fields_selected[1]==83)||($fields_selected[1]==163)||($fields_selected[1]==147)||($fields_selected[1]==99)){
39 print $line; 41 print $line;
42 $empty_file=0;
40 my $bit = $fields_selected[1]; 43 my $bit = $fields_selected[1];
41 if ($bitscore_selected{$bit}){ 44 if ($bitscore_selected{$bit}){
42 $bitscore_selected{$bit}++; 45 $bitscore_selected{$bit}++;
43 } 46 }
44 else { 47 else {
48 } 51 }
49 } 52 }
50 } 53 }
51 54
52 close (IN); 55 close (IN);
53
54 open (LF,">$log_file") or die("Can't open $log_file\n"); 56 open (LF,">$log_file") or die("Can't open $log_file\n");
55 print LF "\n####\t Sam filtering \n"; 57 if ($empty_file==0){
56 print LF "## Before filtering\n"; 58 print LF "\n####\t Sam filtering \n";
57 print LF "bitscore\t:\t"; 59 print LF "## Before filtering\n";
58 foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) { 60 print LF "bitscore\t:\t";
59 print LF $key,"\t*\t"; 61 foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
62 print LF $key,"\t*\t";
63 }
64 print LF "\n number \t:\t";
65 foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
66 print LF $bitscore_all{$key},"\t*\t";
67 }
68 print LF "\n";
69 print LF "## After filtering\n";
70 print LF "bitscore\t:\t";
71 foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
72 print LF $key,"\t*\t";
73 }
74 print LF "\n number \t:\t";
75 foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
76 print LF $bitscore_selected{$key},"\t*\t";
77 }
78 print LF "\n";
60 } 79 }
61 print LF "\n number \t:\t";
62 foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
63 print LF $bitscore_all{$key},"\t*\t";
64 }
65 print LF "\n";
66 print LF "## After filtering\n";
67 print LF "bitscore\t:\t";
68 foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
69 print LF $key,"\t*\t";
70 }
71 print LF "\n number \t:\t";
72 foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
73 print LF $bitscore_selected{$key},"\t*\t";
74 }
75 print LF "\n";
76 close (LF); 80 close (LF);
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