Mercurial > repos > portiahollyoak > temp
comparison scripts/filterFalsePositive.in.pl @ 0:28d1a6f8143f draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
| author | portiahollyoak |
|---|---|
| date | Mon, 25 Apr 2016 13:08:56 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:28d1a6f8143f |
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| 1 #!/share/bin/perl | |
| 2 use List::Util qw(max min); | |
| 3 #system("windowBed -a $ARGV[0] -b /home/wangj2/flycommon/all_transposons.dml.rmskCrossmatch.bed -sw -r 1000 -l 0 > tmp"); | |
| 4 #system("windowBed -a $ARGV[0] -b /home/wangj2/flycommon/soo.trnalnpos.map2.sort.bed -sw -r 1000 -l 0 > tmp"); | |
| 5 system("bedtools window -a $ARGV[0] -b $ARGV[1] -sw -r 1000 -l 0 > tmp"); | |
| 6 | |
| 7 open in,"tmp"; | |
| 8 my %read; | |
| 9 while(<in>) | |
| 10 { | |
| 11 chomp; | |
| 12 split/\t/; | |
| 13 | |
| 14 ## if the same tpye of transposons | |
| 15 my @loc=map { [/(.*?),(\+|-)(.*)/] } split/;/,$_[4]; | |
| 16 foreach my $l (@loc) | |
| 17 { | |
| 18 if($$l[0] eq $_[9]) | |
| 19 { | |
| 20 ## if the same strand of transposons | |
| 21 if((($_[5] eq $$l[1]) && ($_[11] eq "-")) || (($_[5] ne $$l[1]) && ($_[11] eq "+"))) | |
| 22 { | |
| 23 ## if the fragments of the exists transposons | |
| 24 { | |
| 25 my $s=max($$l[2],$_[12]); | |
| 26 my $e=min(($$l[2]+$_[2]-$_[1]),$_[13]); | |
| 27 if($s<$e) | |
| 28 { | |
| 29 print join("\t",@_[0..5]),"\n" if not exists $read{$_[3]}; | |
| 30 $read{$_[3]}=1; | |
| 31 } | |
| 32 } | |
| 33 } | |
| 34 } | |
| 35 } | |
| 36 } | |
| 37 close in; | |
| 38 | |
| 39 system("rm tmp"); |