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1 #!/usr/bin/perl
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2 use Getopt::Long;
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3 # This version includes max_insert_length filtered mapping stat, optionally. (version 2)
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4
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5
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6 my $max_insert_length;
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7 my $readlength;
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8 my $datatype = 'E'; # E or R.
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9 &GetOptions ( 'm|max_insert_length=i' => \$max_insert_length,
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10 'l|readlength=i' => \$readlength,
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11 'd|datatype=s' => \$datatype
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12 );
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13
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14 if(defined($max_insert_length) && !defined($readlength)) { die "readlength (-l|--readlength) must be defined if -m (--max_insert_length) is defined.\n"; }
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15 if(@ARGV<3){ &help; exit; }
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16
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17
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18 my $bowtie = shift @ARGV;
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19 my $sample_name = shift @ARGV;
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20 my $PE = shift @ARGV;
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21
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22 my $prev_head='';
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23 my $NM=0; my $NR=0; my $NM_lf = 0; my $NR_lf = 0; # lf : insert-length-filtered version
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24 my $countNM=0; my $countNM_lf =0;
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25 my $countNR=0; my $countNR_lf = 0;
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26 my $countAll=0; my $countAll_lf=0;
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27
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28
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29 open IN, $bowtie or die "Can't open bowtiefile $bowtie\n";
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30 while(<IN>){
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31 chomp;
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32 my ($head,$tr,$pos1)= (split/\t/)[0,2,3];
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33 if($datatype eq 'R') { ($tr) = (split/\|/,$tr)[3]; $tr=~s/\.\d+$//; }
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34
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35 if($PE==1){
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36 chomp(my $secondline = <IN>);
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37 my ($head2,$pos2) = (split/\t/,$secondline)[0,3];
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38 $head = &min($head,$head2);
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39
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40 }
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41
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42 if($prev_head eq $head) {
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43
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44 if(defined($max_insert_length) && $pos2+$readlength-$pos1 <= $max_insert_length) {
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45 if($tr=~/^NM_/) { $NM_lf = 1; }
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46 elsif($tr=~/^NR_/) { $NR_lf = 1; }
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47 }
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48
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49 if($tr=~/^NM_/) { $NM=1; }
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50 elsif($tr=~/^NR_/) { $NR=1; }
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51 }
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52 else {
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53
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54 if(defined($max_insert_length) && $pos2+$readlength-$pos1 <= $max_insert_length) {
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55 if($NM_lf==1) { $countNM_lf++; $NM_lf=0; }
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56 if($NR_lf==1) { $countNR_lf++; $NR_lf=0; }
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57 $countAll_lf++;
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58 }
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59 if($NM==1) { $countNM++; $NM=0; } ## if a single read is mapped to both NR and NM, it is counted once for each. Therefore total count may not be the same as the sum of NR and NM counts.
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60 if($NR==1) { $countNR++; $NR=0; }
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61 $countAll++;
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62 }
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63 $prev_head=$head;
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64 }
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65 # no need to do additional last line
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66 close IN;
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67
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68
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69 if($datatype eq 'E') { ($countNM,$countNR,$countNM_lf,$countNM_lf) = ('NA','NA','NA','NA'); }
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70
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71 $"="\t";
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72 if(defined($max_insert_length)){
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73 print "sample_name\tmRNA_mapped\tncRNA_mapped\ttotalRNA_mapped\tmRNA_mapped(lenfiltered)\tncRNA_mapped(lenfiltered)\ttotalRNA_mapped(lenfiltered)\n";
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74 print "$sample_name\t$countNM\t$countNR\t$countAll\t$countNM_lf\t$countNR_lf\t$countAll_lf\n";
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75 }
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76 else {
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77 print "sample_name\tmRNA_mapped\tncRNA_mapped\ttotalRNA_mapped\n";
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78 print "$sample_name\t$countNM\t$countNR\t$countAll\n";
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79 }
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80
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81
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82
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83 sub min {
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84 if($_[0] lt $_[1]) { $_[0] } else { $_[1] };
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85 }
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86
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87
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88 sub help {
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89 print STDERR<<EOF;
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90
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91 usage: $0 <options> bowtieoutfile samplename PE(1/0) (> mappingstat)
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92
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93 Options:
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94 -m|--max_insert_length <max_insert_length> : the output includes insert-length-filtered mapping stats as well. -l(--readlength) option must be accompanied. This option is valid only for paired-end data. (For single-end, it is ignored)
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95 -l|--readlength <readlength> : read length. This is required only when -m(--max_insert_length) option is used.
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96 -d|--datatype <datatype> : Either E (Ensembl) or R (Refseq). Use R if the data is Refseq and the transcript names are in format 'gi|xxx|xxx|name'. (Default E)
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97
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98 EOF
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99 }
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100
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101
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102
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103
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